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==========================================================================
  IOBR v0.99.99  Immuno-Oncology Biological Research 
  For Tutorial: https://iobr.github.io/book/
  For Help: https://github.com/IOBR/IOBR/issues

 If you use IOBR in published research, please cite:
 DQ Zeng, YR Fang, ..., GC Yu*, WJ Liao*, 
 Enhancing immuno-oncology investigations through multidimensional decoding 
 of tumor microenvironment with IOBR 2.0. Cell Rep Methods 4, 100910 (2024). 
 &  
 YR Fang, ..., WJ Liao*, DQ Zeng*, 
 Systematic Investigation of Tumor Microenvironment and 
 Antitumor Immunity With IOBR, Med Research (2025). 
 https://onlinelibrary.wiley.com/doi/epdf/10.1002/mdr2.70001 
==========================================================================

Attaching package: ‘zip’

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Loading required package: DBI

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Listening on http://127.0.0.1:33761
Warning in .load_data("anno_grch38") :
  sysdata.rda not found in IOBR package
>>>--- Using variables (anno_grch38) and gene lengths (eff_length)  built into the IOBR package to perform TPM transformation
>>>--- The gene lengths (eff_length) was estimated by function `getGeneLengthAndGCContent` from EDASeq package with default parameters at 2023-02-10
Warning in count2tpm(countMat = data, idType = input$count2tpm_idType, org = input$count2tpm_org,  :
  >>>--- Omit 3985 genes of which length is not available !
>>> log2 transformation was finished
Row number of original eset: 
>>>>  60483
>>> 99.73% of probe in expression set was annotated
Row number after filtering duplicated gene symbol: 
>>>>  50181
>>> log2 transformation was finished
Warning in dir.create(file.path(getwd(), f1), recursive = TRUE) :
  cannot create dir '/srv/shiny-server/IOBRportal/find_outlier_samples_project', reason 'Permission denied'
Warning in dir.create(file.path(getwd(), f1), recursive = TRUE) :
  cannot create dir '/srv/shiny-server/IOBRportal/find_outlier_samples_project', reason 'Permission denied'
Warning in dir.create(file.path(getwd(), f1), recursive = TRUE) :
  cannot create dir '/srv/shiny-server/IOBRportal/find_outlier_samples_project', reason 'Permission denied'
Warning in dir.create(file.path(getwd(), f1), recursive = TRUE) :
  cannot create dir '/srv/shiny-server/IOBRportal/Result_PCA', reason 'Permission denied'
>>>== The two expression matrices share 40745 features in common. 
>>>=== Processing method: sva:: ComBat_seq
Warning in dir.create(file.path(getwd(), f1), recursive = TRUE) :
  cannot create dir '/srv/shiny-server/IOBRportal/Result_PCA', reason 'Permission denied'
>>>== The two expression matrices share 40745 features in common. 
>>>=== Processing method: sva:: ComBat_seq
Row number of original eset: 
>>>>  60483
>>> 0.00% of probe in expression set was annotated
Row number after filtering duplicated gene symbol: 
>>>>  0
Row number of original eset: 
>>>>  60483
>>> 0.00% of probe in expression set was annotated
Row number after filtering duplicated gene symbol: 
>>>>  0
Row number of original eset: 
>>>>  54658
>>> 0.03% of probe in expression set was annotated
Row number after filtering duplicated gene symbol: 
>>>>  16

>>> Calculating signature score using PCA method
>>> log2 transformation was finished
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Warning: In prcomp.default(t(eset), na.action = na.omit, scale. = T) :
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Warning: In prcomp.default(t(eset), na.action = na.omit, scale. = T) :
 extra argument ‘na.action’ will be disregarded
Warning: In prcomp.default(t(eset), na.action = na.omit, scale. = T) :
 extra argument ‘na.action’ will be disregarded
Warning: In prcomp.default(t(eset), na.action = na.omit, scale. = T) :
 extra argument ‘na.action’ will be disregarded
Warning: In prcomp.default(t(eset), na.action = na.omit, scale. = T) :
 extra argument ‘na.action’ will be disregarded
Warning: In prcomp.default(t(eset), na.action = na.omit, scale. = T) :
 extra argument ‘na.action’ will be disregarded
Warning: In prcomp.default(t(eset), na.action = na.omit, scale. = T) :
 extra argument ‘na.action’ will be disregarded
Warning: In prcomp.default(t(eset), na.action = na.omit, scale. = T) :
 extra argument ‘na.action’ will be disregarded
Warning: In prcomp.default(t(eset), na.action = na.omit, scale. = T) :
 extra argument ‘na.action’ will be disregarded
Warning: In prcomp.default(t(eset), na.action = na.omit, scale. = T) :
 extra argument ‘na.action’ will be disregarded
Warning: In prcomp.default(t(eset), na.action = na.omit, scale. = T) :
 extra argument ‘na.action’ will be disregarded
Warning: In prcomp.default(t(eset), na.action = na.omit, scale. = T) :
 extra argument ‘na.action’ will be disregarded
Warning: In prcomp.default(t(eset), na.action = na.omit, scale. = T) :
 extra argument ‘na.action’ will be disregarded
Warning: In prcomp.default(t(eset), na.action = na.omit, scale. = T) :
 extra argument ‘na.action’ will be disregarded
Warning: In prcomp.default(t(eset), na.action = na.omit, scale. = T) :
 extra argument ‘na.action’ will be disregarded
Warning: In prcomp.default(t(eset), na.action = na.omit, scale. = T) :
 extra argument ‘na.action’ will be disregarded
Warning: In prcomp.default(t(eset), na.action = na.omit, scale. = T) :
 extra argument ‘na.action’ will be disregarded
Warning: In prcomp.default(t(eset), na.action = na.omit, scale. = T) :
 extra argument ‘na.action’ will be disregarded

>>> Calculating signature score using ssGSEA method
>>> log2 transformation was finished

>>> Calculating signature score using ssGSEA method
>>> log2 transformation was finished

>>> Calculating signature score using z-score method
>>> log2 transformation was finished

>>> Calculating signature score using z-score method
>>> log2 transformation was finished

>>> Running CIBERSORT

>>> Running EPIC
Warning in IOBR::EPIC(bulk = eset, reference = ref, mRNA_cell = NULL, scaleExprs = TRUE) :
  mRNA_cell value unknown for some cell types: CAFs, Endothelial - using the default value of 0.4 for these but this might bias the true cell proportions from all cell types.

Running quanTIseq deconvolution module

Gene expression normalization and re-annotation (arrays: FALSE)

Removing 17 noisy genes

Removing 15 genes with high expression in tumors

Signature genes found in data set: 137/138 (99.28%)

Mixture deconvolution (method: lsei)

Deconvolution sucessful!

>>> Running xCell

>>> Running xCell

>>> Running ESTIMATE
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '-eset.txt': Permission denied

>>> Running xCell

>>> Running ESTIMATE
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '-eset.txt': Permission denied
## Enter batch mode


## Loading immune gene expression

## Removing the batch effect of /tmp/RtmpjDGCzd/file13be04f0ef54c

## Enter batch mode


## Loading immune gene expression

## Removing the batch effect of /tmp/RtmpjDGCzd/file13be05996348b


>>> Running MCP-counter

>>> Running Immunophenoscore
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
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Warning in cor.test.default(x, data[, target], method = method) :
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Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
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Warning in cor.test.default(x, data[, target], method = method) :
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Warning in cor.test.default(x, data[, target], method = method) :
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Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
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Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
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Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
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Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in cor.test.default(x, data[, target], method = method) :
  Cannot compute exact p-value with ties
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights,  :
  Loglik converged before variable  1 ; coefficient may be infinite. 
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights,  :
  Loglik converged before variable  1 ; coefficient may be infinite. 
>>>-- Grouping information: 
>>>-- Grouping information: 
>>>-- Grouping information: 
>>>-- Grouping information: 
>>>-- Grouping information: 
>>>-- Grouping information: 
Warning in dir.create(file_store) :
  cannot create dir '1-Subtype-relevant-varbiles-heatmap', reason 'Permission denied'
tidyHeatmap says: (once per session) from release 1.7.0 the scaling is set to "none" by default. Please use scale = "row", "column" or "both" to apply scaling
tidyHeatmap says: If you use tidyHeatmap for scientific research, please cite: Mangiola, S. and Papenfuss, A.T., 2020. 'tidyHeatmap: an R package for modular heatmap production based on tidy principles.' Journal of Open Source Software. doi:10.21105/joss.02472.
This message is displayed once per session.
Warning: `when()` was deprecated in purrr 1.0.0.
ℹ Please use `if` instead.
ℹ The deprecated feature was likely used in the tidyHeatmap package.
  Please report the issue at
  <https://github.com/stemangiola/tidyHeatmap/issues>.
Warning in dir.create(file_store) :
  cannot create dir '1-Subtype-relevant-varbiles-heatmap', reason 'Permission denied'
Warning in dir.create(file_store) :
  cannot create dir '1-Subtype-relevant-varbiles-heatmap', reason 'Permission denied'
Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
ℹ The deprecated feature was likely used in the IOBR package.
  Please report the issue at <https://github.com/IOBR/IOBR/issues>.
There are seven categories you can choose: box, continue2, continue, random, heatmap, heatmap3, tidyheatmap 
There are ten palettes you can choose: nrc, jama, aaas, jco, paired1-4, accent, set2
>>>>Options for `theme`: light, bw, classic and classic2
There are seven categories you can choose: box, continue2, continue, random, heatmap, heatmap3, tidyheatmap 
>>>>=== Palette option for random: 1: palette1; 2: palette2; 3: palette3;  4: palette4
Top 10 signatures will be shown
Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
ℹ The deprecated feature was likely used in the ggplot2 package.
  Please report the issue at <https://github.com/tidyverse/ggplot2/issues>.
`height` was translated to `width`.
Warning in cor.test.default(data[, var1], data[, var2], method = method) :
  Cannot compute exact p-value with ties
>>>>Options for `theme`: light, bw, classic and classic2
`geom_smooth()` using formula = 'y ~ x'
Warning in dir.create(file.path(getwd(), f1), recursive = TRUE) :
  cannot create dir '/srv/shiny-server/IOBRportal/1-Cor-of-B_cells_memory_CIBERSORT-and-Macrophages_M2_CIBERSORT', reason 'Permission denied'
`geom_smooth()` using formula = 'y ~ x'
Warning in dir.create(file.path(getwd(), f1), recursive = TRUE) :
  cannot create dir '/srv/shiny-server/IOBRportal/1-cor_matrix_plot', reason 'Permission denied'
Warning in dir.create(file.path(getwd(), f1), recursive = TRUE) :
  cannot create dir '/srv/shiny-server/IOBRportal/1-cor_matrix_plot', reason 'Permission denied'
Warning in dir.create(file.path(getwd(), f1), recursive = TRUE) :
  cannot create dir '/srv/shiny-server/IOBRportal/1-cor_matrix_plot', reason 'Permission denied'
Warning in dir.create(save_path) :
  cannot create dir 'KMplot', reason 'Permission denied'
>>> Dataset's survival follow up time is range between 0.1 to 124 months
Warning in gzfile(file, "wb") :
  cannot open compressed file '/srv/shiny-server/IOBRportal/KMplot/0--Subtype-survival-analysis-input.RData', probable reason 'No such file or directory'
Warning in dir.create(save_path) :
  cannot create dir 'KMplot', reason 'Permission denied'
>>> Dataset's survival follow up time is range between 0.1 to 124 months
Warning in gzfile(file, "wb") :
  cannot open compressed file '/srv/shiny-server/IOBRportal/KMplot/0--TMEscore_binary-survival-analysis-input.RData', probable reason 'No such file or directory'
Warning in dir.create(save_path) :
  cannot create dir 'KMplot', reason 'Permission denied'
>>> Dataset's survival follow up time is range between 0.1 to 124 months
Warning in gzfile(file, "wb") :
  cannot open compressed file '/srv/shiny-server/IOBRportal/KMplot/0--TMEscore_binary-survival-analysis-input.RData', probable reason 'No such file or directory'
Warning in dir.create(save_path) :
  cannot create dir 'KM-plot', reason 'Permission denied'
>>> Dataset's survival follow up time is range between 0.1 to 124 months
>>> The best cutoff for B-cells-memory is: 0.01
>>>-- The best cutoff is =  0.013376138
>>> High  B-cells-memory  =  79 
>>> Low  B-cells-memory  =  271 
Warning in gzfile(file, "wb") :
  cannot open compressed file '/srv/shiny-server/IOBRportal/KM-plot/1-0-KM-B-cells-memory-survival-analysis-input.RData', probable reason 'No such file or directory'
Warning in dir.create(save_path) :
  cannot create dir 'KM-plot', reason 'Permission denied'
>>> Dataset's survival follow up time is range between 0.1 to 124 months
>>> The best cutoff for B-cells-memory is: 0.01
>>>-- The best cutoff is =  0.013376138
>>> High  B-cells-memory  =  79 
>>> Low  B-cells-memory  =  271 
Warning in gzfile(file, "wb") :
  cannot open compressed file '/srv/shiny-server/IOBRportal/KM-plot/1-0-KM-B-cells-memory-survival-analysis-input.RData', probable reason 'No such file or directory'
>>>== head of input data: 
>>>== head of input data: 
Warning in dir.create(file.path(getwd(), f1), recursive = TRUE) :
  cannot create dir '/srv/shiny-server/IOBRportal/ROC-time', reason 'Permission denied'
>>=== Predicting combined score...
Warning in read.table(input$iobr_deg_input2$datapath, header = TRUE, sep = "\t",  :
  line 1 appears to contain embedded nulls
Warning in read.table(input$iobr_deg_input2$datapath, header = TRUE, sep = "\t",  :
  line 3 appears to contain embedded nulls
Warning in read.table(input$iobr_deg_input2$datapath, header = TRUE, sep = "\t",  :
  line 4 appears to contain embedded nulls
Warning in read.table(input$iobr_deg_input2$datapath, header = TRUE, sep = "\t",  :
  line 1 appears to contain embedded nulls
Warning in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :
  embedded nul(s) found in input
Warning in read.table(input$iobr_deg_input1$datapath, row.names = 1, sep = "\t",  :
  line 1 appears to contain embedded nulls
Warning in read.table(input$iobr_deg_input1$datapath, row.names = 1, sep = "\t",  :
  line 3 appears to contain embedded nulls
Warning in read.table(input$iobr_deg_input1$datapath, row.names = 1, sep = "\t",  :
  line 4 appears to contain embedded nulls
Warning in read.table(input$iobr_deg_input1$datapath, row.names = 1, sep = "\t",  :
  line 5 appears to contain embedded nulls
Warning in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :
  embedded nul(s) found in input
Warning in read.table(input$iobr_deg_input2$datapath, header = TRUE, sep = "\t",  :
  line 1 appears to contain embedded nulls
Warning in read.table(input$iobr_deg_input2$datapath, header = TRUE, sep = "\t",  :
  line 3 appears to contain embedded nulls
Warning in read.table(input$iobr_deg_input2$datapath, header = TRUE, sep = "\t",  :
  line 4 appears to contain embedded nulls
Warning in read.table(input$iobr_deg_input2$datapath, header = TRUE, sep = "\t",  :
  line 1 appears to contain embedded nulls
Warning in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :
  embedded nul(s) found in input
Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-')
Using Seurat v5+ workflow
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix

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Finding variable features for layer counts
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Warning in svd.function(A = t(x = object), nv = npcs, ...) :
  You're computing too large a percentage of total singular values, use a standard svd instead.
PC_ 1 
Positive:  DMPK, NEGR1, MYLK, CSPG4, CNN1, FOXP2, CACNA1H, DNAJB5, PGM5, JPH2 
	   LMOD1, DACT3, ASB2, CAV1, SPEG, MTURN, FENDRR, RBPMS2, SYNM, RP11-554A11.5 
	   PRICKLE2, TSPAN18, SORBS1, FBXL22, CAP2, EML1, NPTXR, FERMT2, ACTG2, ANGPTL1 
Negative:  TSPAN13, BMP2, MAL2, CDC6, SPINT2, C12orf75, BAIAP2L1, SPINT1, ATP2C1, KCNK1 
	   UNC5CL, SLC9A7, MANEAL, CDH1, NFE2L3, HN1, SLCO4A1, LSR, STIL, LRRC16A 
	   RASSF7, CLDN4, SPINK1, CDCP1, HELZ2, RIPK4, CTSH, ETV7, PLS1, BRI3BP 
PC_ 2 
Positive:  IGHV5-51, IGHV3-23, FAM46C, IGLV3-21, IGHV3-21, IGHV1-46, IGKV3-20, IGHV4-34, CTSW, IGHV3-30 
	   IGLV3-1, IGLC2, IGLV2-11, IGHJ3, IGHV3-74, IGLL5, IGLV1-44, IGKV3D-11, IGKV3-15, IGHV3OR16-8 
	   IGKV3-7, PIM2, IGHV3-7, IGHV1-17, IGHV3-72, IGLV7-46, SPAG4, IGHV1-18, IGKV3D-20, IGHG2 
Negative:  KLK11, SNORD39, ILDR1, AKR1C2, MTND4P24, GJB5, DSG3, TRIM29, FGFBP1, AKR1C1 
	   MUC3A, AC069213.1, GJB4, FUT3, CLDN10-AS1, ANXA8L1, NPC1L1, SBSN, ANXA8, KRT17 
	   SPRR1B, NPY6R, CALML3, PDZK1, SPRR2A, RP11-223C24.2, SERPINE3, SPRR2D, KRT6A, SPRR2E 
PC_ 3 
Positive:  NCAM1, GLB1L2, TRPM5, KLHL13, KIAA1324, HEPACAM2, GAMT, SLC2A10, C15orf48, ARHGAP5-AS1 
	   AP000439.3, RNA5-8SP6, 5-8S-rRNA, NMU, GC, FKBP1B, RPS3AP5, KRT81, PTPN18, LINC00675 
	   SLC43A3, RGS13, FBP1, FOXI1, AVIL, APOH, RASSF10, RP11-778D9.4, CDH12, GLYATL2 
Negative:  ERAP2, CAPN8, CYP2C18, ONECUT3, IGHV4-39, GAL3ST1, GJB1, IGKV2-26, PLEKHG4, BLACAT1 
	   MIR4537, ANKRD36BP2, LEMD1, KLHDC7A, FOXA3, LAX1, SLC6A14, SYT13, IGHG4, IGKV5-2 
	   IGKV2D-24, IGHV3-64, IGHJ3P, IGKV1-16, LAMA3, IGKV2-30, APOBEC3B, IGLC3, RIN1, IGLJ3 
PC_ 4 
Positive:  B3GALT5, CES2, HTR1D, GAL3ST2, SULT1B1, ANPEP, AL901608.1, SI, CLDN15, ALDOB 
	   CHP2, PLAC8, TMEM150B, GPA33, MOGAT2, NAT2, CYP3A4, RP11-102C16.3, HMGA1P5, KCNJ3 
	   TUBAL3, MT1H, C10orf99, AC000111.6, PPP1R14D, ATP10B, CDX1, NOS2, B4GALNT2, CDX2 
Negative:  RP11-110G21.2, RNU4-62P, RNA5SP498, RNU6-758P, RNU4-40P, RNU6-1016P, RNU6-37P, RNY4P34, snoU13, MIR126 
	   RNU6-437P, MT-TY, RNU7-45P, RNU7-41P, RNU6-194P, RNU6-130P, RP11-475J5.6, CT83, RNU4-80P, KRT7 
	   RNU6-530P, RNA5SP84, MIR6801, RNU6-937P, MTND6P3, RNA5SP92, MIR5690, MIR199B, RNA5SP367, RNU6-321P 
PC_ 5 
Positive:  GABRP, SERPINB2, AC016735.2, IGLV1-41, IGHV3-38, RSAD2, IGKV2-29, IGKV1D-13, CTD-3018O17.5, IGKV1OR2-6 
	   IGKV1-13, MIR4316, RP11-412H8.2, CALB1, OASL, IGHV3-6, ANXA10, HRASLS2, IGKV6-21, BACE2 
	   IGHV3-35, RP11-457P14.6, DLGAP1-AS5, HOXC10, IGHV1OR16-1, MIR6731, IGHD4-17, CEACAM7, RASAL1, MIR664A 
Negative:  MIR559, TMEM82, ODAM, REG3A, DEFA6, PGA5, RNU7-14P, RNU7-97P, ATP4B, PGA3 
	   ATP4A, DEFA5, RP11-345K20.2, FAM3D, IGHD5-24, RPSAP8, RNU6-322P, RP1-68D18.4, RP11-789C1.2, BTNL8 
	   AADAC, SCGN, FOSB, APOLD1, SNORD116-12, SLC10A2, RNU6-14P, PRODH, RP11-64D22.5, RNU1-80P 
Calculating cluster EBV
For a (much!) faster implementation of the Wilcoxon Rank Sum Test,
(default method for FindMarkers) please install the presto package
--------------------------------------------
install.packages('devtools')
devtools::install_github('immunogenomics/presto')
--------------------------------------------
After installation of presto, Seurat will automatically use the more 
efficient implementation (no further action necessary).
This message will be shown once per session
Calculating cluster GS
Final groups for plot: 2 -> EBV, GS
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Warning: Removed 5 rows containing missing values or values outside the scale range
(`geom_point()`).
Final groups for plot: 2 -> Negitive, Positive
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Warning: Removed 5 rows containing missing values or values outside the scale range
(`geom_point()`).
Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-')
Using Seurat v5+ workflow
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix

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Finding variable features for layer counts
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Warning in svd.function(A = t(x = object), nv = npcs, ...) :
  You're computing too large a percentage of total singular values, use a standard svd instead.
PC_ 1 
Positive:  DMPK, NEGR1, MYLK, CSPG4, CNN1, FOXP2, CACNA1H, DNAJB5, PGM5, JPH2 
	   LMOD1, DACT3, ASB2, CAV1, SPEG, MTURN, FENDRR, RBPMS2, SYNM, RP11-554A11.5 
	   PRICKLE2, TSPAN18, SORBS1, FBXL22, CAP2, EML1, NPTXR, FERMT2, ACTG2, ANGPTL1 
Negative:  TSPAN13, BMP2, MAL2, CDC6, SPINT2, C12orf75, BAIAP2L1, SPINT1, ATP2C1, KCNK1 
	   UNC5CL, SLC9A7, MANEAL, CDH1, NFE2L3, HN1, SLCO4A1, LSR, STIL, LRRC16A 
	   RASSF7, CLDN4, SPINK1, CDCP1, HELZ2, RIPK4, CTSH, ETV7, PLS1, BRI3BP 
PC_ 2 
Positive:  IGHV5-51, IGHV3-23, FAM46C, IGLV3-21, IGHV3-21, IGHV1-46, IGKV3-20, IGHV4-34, CTSW, IGHV3-30 
	   IGLV3-1, IGLC2, IGLV2-11, IGHJ3, IGHV3-74, IGLL5, IGLV1-44, IGKV3D-11, IGKV3-15, IGHV3OR16-8 
	   IGKV3-7, PIM2, IGHV3-7, IGHV1-17, IGHV3-72, IGLV7-46, SPAG4, IGHV1-18, IGKV3D-20, IGHG2 
Negative:  KLK11, SNORD39, ILDR1, AKR1C2, MTND4P24, GJB5, DSG3, TRIM29, FGFBP1, AKR1C1 
	   MUC3A, AC069213.1, GJB4, FUT3, CLDN10-AS1, ANXA8L1, NPC1L1, SBSN, ANXA8, KRT17 
	   SPRR1B, NPY6R, CALML3, PDZK1, SPRR2A, RP11-223C24.2, SERPINE3, SPRR2D, KRT6A, SPRR2E 
PC_ 3 
Positive:  NCAM1, GLB1L2, TRPM5, KLHL13, KIAA1324, HEPACAM2, GAMT, SLC2A10, C15orf48, ARHGAP5-AS1 
	   AP000439.3, RNA5-8SP6, 5-8S-rRNA, NMU, GC, FKBP1B, RPS3AP5, KRT81, PTPN18, LINC00675 
	   SLC43A3, RGS13, FBP1, FOXI1, AVIL, APOH, RASSF10, RP11-778D9.4, CDH12, GLYATL2 
Negative:  ERAP2, CAPN8, CYP2C18, ONECUT3, IGHV4-39, GAL3ST1, GJB1, IGKV2-26, PLEKHG4, BLACAT1 
	   MIR4537, ANKRD36BP2, LEMD1, KLHDC7A, FOXA3, LAX1, SLC6A14, SYT13, IGHG4, IGKV5-2 
	   IGKV2D-24, IGHV3-64, IGHJ3P, IGKV1-16, LAMA3, IGKV2-30, APOBEC3B, IGLC3, RIN1, IGLJ3 
PC_ 4 
Positive:  B3GALT5, CES2, HTR1D, GAL3ST2, SULT1B1, ANPEP, AL901608.1, SI, CLDN15, ALDOB 
	   CHP2, PLAC8, TMEM150B, GPA33, MOGAT2, NAT2, CYP3A4, RP11-102C16.3, HMGA1P5, KCNJ3 
	   TUBAL3, MT1H, C10orf99, AC000111.6, PPP1R14D, ATP10B, CDX1, NOS2, B4GALNT2, CDX2 
Negative:  RP11-110G21.2, RNU4-62P, RNA5SP498, RNU6-758P, RNU4-40P, RNU6-1016P, RNU6-37P, RNY4P34, snoU13, MIR126 
	   RNU6-437P, MT-TY, RNU7-45P, RNU7-41P, RNU6-194P, RNU6-130P, RP11-475J5.6, CT83, RNU4-80P, KRT7 
	   RNU6-530P, RNA5SP84, MIR6801, RNU6-937P, MTND6P3, RNA5SP92, MIR5690, MIR199B, RNA5SP367, RNU6-321P 
PC_ 5 
Positive:  GABRP, SERPINB2, AC016735.2, IGLV1-41, IGHV3-38, RSAD2, IGKV2-29, IGKV1D-13, CTD-3018O17.5, IGKV1OR2-6 
	   IGKV1-13, MIR4316, RP11-412H8.2, CALB1, OASL, IGHV3-6, ANXA10, HRASLS2, IGKV6-21, BACE2 
	   IGHV3-35, RP11-457P14.6, DLGAP1-AS5, HOXC10, IGHV1OR16-1, MIR6731, IGHD4-17, CEACAM7, RASAL1, MIR664A 
Negative:  MIR559, TMEM82, ODAM, REG3A, DEFA6, PGA5, RNU7-14P, RNU7-97P, ATP4B, PGA3 
	   ATP4A, DEFA5, RP11-345K20.2, FAM3D, IGHD5-24, RPSAP8, RNU6-322P, RP1-68D18.4, RP11-789C1.2, BTNL8 
	   AADAC, SCGN, FOSB, APOLD1, SNORD116-12, SLC10A2, RNU6-14P, PRODH, RP11-64D22.5, RNU1-80P 
Calculating cluster Positive
Calculating cluster Negitive
Final groups for plot: 2 -> Negitive, Positive
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Warning: Removed 5 rows containing missing values or values outside the scale range
(`geom_point()`).
Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-')
Using Seurat v5+ workflow
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix

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Finding variable features for layer counts
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Warning in svd.function(A = t(x = object), nv = npcs, ...) :
  You're computing too large a percentage of total singular values, use a standard svd instead.
PC_ 1 
Positive:  DMPK, NEGR1, MYLK, CSPG4, CNN1, FOXP2, CACNA1H, DNAJB5, PGM5, JPH2 
	   LMOD1, DACT3, ASB2, CAV1, SPEG, MTURN, FENDRR, RBPMS2, SYNM, RP11-554A11.5 
	   PRICKLE2, TSPAN18, SORBS1, FBXL22, CAP2, EML1, NPTXR, FERMT2, ACTG2, ANGPTL1 
Negative:  TSPAN13, BMP2, MAL2, CDC6, SPINT2, C12orf75, BAIAP2L1, SPINT1, ATP2C1, KCNK1 
	   UNC5CL, SLC9A7, MANEAL, CDH1, NFE2L3, HN1, SLCO4A1, LSR, STIL, LRRC16A 
	   RASSF7, CLDN4, SPINK1, CDCP1, HELZ2, RIPK4, CTSH, ETV7, PLS1, BRI3BP 
PC_ 2 
Positive:  IGHV5-51, IGHV3-23, FAM46C, IGLV3-21, IGHV3-21, IGHV1-46, IGKV3-20, IGHV4-34, CTSW, IGHV3-30 
	   IGLV3-1, IGLC2, IGLV2-11, IGHJ3, IGHV3-74, IGLL5, IGLV1-44, IGKV3D-11, IGKV3-15, IGHV3OR16-8 
	   IGKV3-7, PIM2, IGHV3-7, IGHV1-17, IGHV3-72, IGLV7-46, SPAG4, IGHV1-18, IGKV3D-20, IGHG2 
Negative:  KLK11, SNORD39, ILDR1, AKR1C2, MTND4P24, GJB5, DSG3, TRIM29, FGFBP1, AKR1C1 
	   MUC3A, AC069213.1, GJB4, FUT3, CLDN10-AS1, ANXA8L1, NPC1L1, SBSN, ANXA8, KRT17 
	   SPRR1B, NPY6R, CALML3, PDZK1, SPRR2A, RP11-223C24.2, SERPINE3, SPRR2D, KRT6A, SPRR2E 
PC_ 3 
Positive:  NCAM1, GLB1L2, TRPM5, KLHL13, KIAA1324, HEPACAM2, GAMT, SLC2A10, C15orf48, ARHGAP5-AS1 
	   AP000439.3, RNA5-8SP6, 5-8S-rRNA, NMU, GC, FKBP1B, RPS3AP5, KRT81, PTPN18, LINC00675 
	   SLC43A3, RGS13, FBP1, FOXI1, AVIL, APOH, RASSF10, RP11-778D9.4, CDH12, GLYATL2 
Negative:  ERAP2, CAPN8, CYP2C18, ONECUT3, IGHV4-39, GAL3ST1, GJB1, IGKV2-26, PLEKHG4, BLACAT1 
	   MIR4537, ANKRD36BP2, LEMD1, KLHDC7A, FOXA3, LAX1, SLC6A14, SYT13, IGHG4, IGKV5-2 
	   IGKV2D-24, IGHV3-64, IGHJ3P, IGKV1-16, LAMA3, IGKV2-30, APOBEC3B, IGLC3, RIN1, IGLJ3 
PC_ 4 
Positive:  B3GALT5, CES2, HTR1D, GAL3ST2, SULT1B1, ANPEP, AL901608.1, SI, CLDN15, ALDOB 
	   CHP2, PLAC8, TMEM150B, GPA33, MOGAT2, NAT2, CYP3A4, RP11-102C16.3, HMGA1P5, KCNJ3 
	   TUBAL3, MT1H, C10orf99, AC000111.6, PPP1R14D, ATP10B, CDX1, NOS2, B4GALNT2, CDX2 
Negative:  RP11-110G21.2, RNU4-62P, RNA5SP498, RNU6-758P, RNU4-40P, RNU6-1016P, RNU6-37P, RNY4P34, snoU13, MIR126 
	   RNU6-437P, MT-TY, RNU7-45P, RNU7-41P, RNU6-194P, RNU6-130P, RP11-475J5.6, CT83, RNU4-80P, KRT7 
	   RNU6-530P, RNA5SP84, MIR6801, RNU6-937P, MTND6P3, RNA5SP92, MIR5690, MIR199B, RNA5SP367, RNU6-321P 
PC_ 5 
Positive:  GABRP, SERPINB2, AC016735.2, IGLV1-41, IGHV3-38, RSAD2, IGKV2-29, IGKV1D-13, CTD-3018O17.5, IGKV1OR2-6 
	   IGKV1-13, MIR4316, RP11-412H8.2, CALB1, OASL, IGHV3-6, ANXA10, HRASLS2, IGKV6-21, BACE2 
	   IGHV3-35, RP11-457P14.6, DLGAP1-AS5, HOXC10, IGHV1OR16-1, MIR6731, IGHD4-17, CEACAM7, RASAL1, MIR664A 
Negative:  MIR559, TMEM82, ODAM, REG3A, DEFA6, PGA5, RNU7-14P, RNU7-97P, ATP4B, PGA3 
	   ATP4A, DEFA5, RP11-345K20.2, FAM3D, IGHD5-24, RPSAP8, RNU6-322P, RP1-68D18.4, RP11-789C1.2, BTNL8 
	   AADAC, SCGN, FOSB, APOLD1, SNORD116-12, SLC10A2, RNU6-14P, PRODH, RP11-64D22.5, RNU1-80P 
Calculating cluster Positive
Calculating cluster Negitive
Final groups for plot: 2 -> Negitive, Positive
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Warning: Removed 5 rows containing missing values or values outside the scale range
(`geom_point()`).
Final groups for plot: 2 -> EBV, GS
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Warning: Removed 5 rows containing missing values or values outside the scale range
(`geom_point()`).
Using Seurat v5+ workflow
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix

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Finding variable features for layer counts
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Warning in svd.function(A = t(x = object), nv = npcs, ...) :
  You're computing too large a percentage of total singular values, use a standard svd instead.
PC_ 1 
Positive:  ENSG00000125845, ENSG00000094804, ENSG00000168394, ENSG00000166145, ENSG00000106537, ENSG00000006453, ENSG00000132646, ENSG00000137648, ENSG00000147676, ENSG00000167642 
	   ENSG00000235162, ENSG00000183421, ENSG00000109861, ENSG00000103811, ENSG00000185090, ENSG00000140406, ENSG00000135750, ENSG00000198829, ENSG00000008517, ENSG00000176153 
	   ENSG00000114805, ENSG00000136295, ENSG00000196975, ENSG00000189159, ENSG00000189143, ENSG00000176597, ENSG00000166803, ENSG00000101003, ENSG00000124602, ENSG00000188112 
Negative:  ENSG00000196557, ENSG00000095637, ENSG00000066629, ENSG00000182253, ENSG00000083290, ENSG00000131831, ENSG00000154330, ENSG00000173546, ENSG00000077782, ENSG00000163431 
	   ENSG00000154553, ENSG00000072952, ENSG00000121898, ENSG00000182568, ENSG00000072195, ENSG00000172260, ENSG00000128573, ENSG00000198947, ENSG00000183741, ENSG00000197380 
	   ENSG00000187391, ENSG00000128591, ENSG00000166313, ENSG00000135424, ENSG00000268388, ENSG00000112320, ENSG00000104936, ENSG00000180354, ENSG00000121440, ENSG00000149596 
PC_ 2 
Positive:  ENSG00000187134, ENSG00000171124, ENSG00000169894, ENSG00000169903, ENSG00000168743, ENSG00000107159, ENSG00000167741, ENSG00000151632, ENSG00000164099, ENSG00000134757 
	   ENSG00000189280, ENSG00000137699, ENSG00000244734, ENSG00000184434, ENSG00000172264, ENSG00000015520, ENSG00000009950, ENSG00000174469, ENSG00000081277, ENSG00000170835 
	   ENSG00000142661, ENSG00000181409, ENSG00000224769, ENSG00000189433, ENSG00000169876, ENSG00000174827, ENSG00000176945, ENSG00000081800, ENSG00000106384, ENSG00000106688 
Negative:  ENSG00000066405, ENSG00000241351, ENSG00000173578, ENSG00000159263, ENSG00000243466, ENSG00000211962, ENSG00000102096, ENSG00000163888, ENSG00000119919, ENSG00000164690 
	   ENSG00000163735, ENSG00000148735, ENSG00000147257, ENSG00000270550, ENSG00000139044, ENSG00000211899, ENSG00000239951, ENSG00000211669, ENSG00000211947, ENSG00000022556 
	   ENSG00000124664, ENSG00000100918, ENSG00000088992, ENSG00000184012, ENSG00000175538, ENSG00000211966, ENSG00000165905, ENSG00000163734, ENSG00000148702, ENSG00000169347 
PC_ 3 
Positive:  ENSG00000274422, ENSG00000270906, ENSG00000124107, ENSG00000160183, ENSG00000196091, ENSG00000145864, ENSG00000205922, ENSG00000230387, ENSG00000157502, ENSG00000029534 
	   ENSG00000133433, ENSG00000270909, ENSG00000204019, ENSG00000196436, ENSG00000137558, ENSG00000126709, ENSG00000235020, ENSG00000012223, ENSG00000247627, ENSG00000232721 
	   ENSG00000270154, ENSG00000137959, ENSG00000185290, ENSG00000144644, ENSG00000198744, ENSG00000089327, ENSG00000129451, ENSG00000279304, ENSG00000094755, ENSG00000136881 
Negative:  ENSG00000117983, ENSG00000187210, ENSG00000107807, ENSG00000036473, ENSG00000153823, ENSG00000100889, ENSG00000175344, ENSG00000118513, ENSG00000133477, ENSG00000164237 
	   ENSG00000115255, ENSG00000099617, ENSG00000278535, ENSG00000263429, ENSG00000166920, ENSG00000169715, ENSG00000198576, ENSG00000116771, ENSG00000125144, ENSG00000156966 
	   ENSG00000112494, ENSG00000161267, ENSG00000118322, ENSG00000224826, ENSG00000135097, ENSG00000116299, ENSG00000138823, ENSG00000124253, ENSG00000162482, ENSG00000178035 
PC_ 4 
Positive:  ENSG00000232216, ENSG00000064651, ENSG00000160182, ENSG00000241755, ENSG00000115386, ENSG00000211950, ENSG00000114248, ENSG00000143297, ENSG00000211893, ENSG00000275395 
	   ENSG00000105523, ENSG00000171747, ENSG00000211639, ENSG00000253691, ENSG00000254157, ENSG00000198099, ENSG00000211959, ENSG00000163618, ENSG00000131620, ENSG00000182938 
	   ENSG00000211938, ENSG00000271178, ENSG00000163751, ENSG00000211946, ENSG00000132465, ENSG00000099834, ENSG00000198910, ENSG00000260048, ENSG00000211666, ENSG00000112297 
Negative:  ENSG00000215030, ENSG00000069535, ENSG00000164070, ENSG00000003096, ENSG00000197172, ENSG00000236283, ENSG00000163032, ENSG00000258655, ENSG00000254471, ENSG00000261159 
	   ENSG00000196482, ENSG00000267924, ENSG00000274150, ENSG00000229835, ENSG00000186094, ENSG00000182263, ENSG00000198681, ENSG00000119782, ENSG00000185053, ENSG00000178568 
	   ENSG00000221867, ENSG00000242741, ENSG00000156284, ENSG00000156689, ENSG00000154162, ENSG00000178690, ENSG00000121388, ENSG00000281655, ENSG00000127074, ENSG00000205426 
PC_ 5 
Positive:  ENSG00000088882, ENSG00000113083, ENSG00000095752, ENSG00000154096, ENSG00000129988, ENSG00000106366, ENSG00000133048, ENSG00000170323, ENSG00000149968, ENSG00000181092 
	   ENSG00000148848, ENSG00000133488, ENSG00000166819, ENSG00000081041, ENSG00000143320, ENSG00000188257, ENSG00000214548, ENSG00000108342, ENSG00000176194, ENSG00000145536 
	   ENSG00000128510, ENSG00000257017, ENSG00000116690, ENSG00000183072, ENSG00000109705, ENSG00000187288, ENSG00000163394, ENSG00000182585, ENSG00000230615, ENSG00000173432 
Negative:  ENSG00000181617, ENSG00000174944, ENSG00000117322, ENSG00000249599, ENSG00000164176, ENSG00000249082, ENSG00000159307, ENSG00000129451, ENSG00000130222, ENSG00000156234 
	   ENSG00000262319, ENSG00000278928, ENSG00000221112, ENSG00000166509, ENSG00000167656, ENSG00000121769, ENSG00000105369, ENSG00000171885, ENSG00000163884, ENSG00000230778 
	   ENSG00000172987, ENSG00000133454, ENSG00000073067, ENSG00000103175, ENSG00000164764, ENSG00000138100, ENSG00000229314, ENSG00000156738, ENSG00000077943, ENSG00000236466 
Calculating cluster EBV
Calculating cluster GS
Warning: No DE genes identified
Using Seurat v5+ workflow
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix

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Finding variable features for layer counts
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Warning in svd.function(A = t(x = object), nv = npcs, ...) :
  You're computing too large a percentage of total singular values, use a standard svd instead.
PC_ 1 
Positive:  ENSG00000125845, ENSG00000094804, ENSG00000168394, ENSG00000166145, ENSG00000106537, ENSG00000006453, ENSG00000132646, ENSG00000137648, ENSG00000147676, ENSG00000167642 
	   ENSG00000235162, ENSG00000183421, ENSG00000109861, ENSG00000103811, ENSG00000185090, ENSG00000140406, ENSG00000135750, ENSG00000198829, ENSG00000008517, ENSG00000176153 
	   ENSG00000114805, ENSG00000136295, ENSG00000196975, ENSG00000189159, ENSG00000189143, ENSG00000176597, ENSG00000166803, ENSG00000101003, ENSG00000124602, ENSG00000188112 
Negative:  ENSG00000196557, ENSG00000095637, ENSG00000066629, ENSG00000182253, ENSG00000083290, ENSG00000131831, ENSG00000154330, ENSG00000173546, ENSG00000077782, ENSG00000163431 
	   ENSG00000154553, ENSG00000072952, ENSG00000121898, ENSG00000182568, ENSG00000072195, ENSG00000172260, ENSG00000128573, ENSG00000198947, ENSG00000183741, ENSG00000197380 
	   ENSG00000187391, ENSG00000128591, ENSG00000166313, ENSG00000135424, ENSG00000268388, ENSG00000112320, ENSG00000104936, ENSG00000180354, ENSG00000121440, ENSG00000149596 
PC_ 2 
Positive:  ENSG00000187134, ENSG00000171124, ENSG00000169894, ENSG00000169903, ENSG00000168743, ENSG00000107159, ENSG00000167741, ENSG00000151632, ENSG00000164099, ENSG00000134757 
	   ENSG00000189280, ENSG00000137699, ENSG00000244734, ENSG00000184434, ENSG00000172264, ENSG00000015520, ENSG00000009950, ENSG00000174469, ENSG00000081277, ENSG00000170835 
	   ENSG00000142661, ENSG00000181409, ENSG00000224769, ENSG00000189433, ENSG00000169876, ENSG00000174827, ENSG00000176945, ENSG00000081800, ENSG00000106384, ENSG00000106688 
Negative:  ENSG00000066405, ENSG00000241351, ENSG00000173578, ENSG00000159263, ENSG00000243466, ENSG00000211962, ENSG00000102096, ENSG00000163888, ENSG00000119919, ENSG00000164690 
	   ENSG00000163735, ENSG00000148735, ENSG00000147257, ENSG00000270550, ENSG00000139044, ENSG00000211899, ENSG00000239951, ENSG00000211669, ENSG00000211947, ENSG00000022556 
	   ENSG00000124664, ENSG00000100918, ENSG00000088992, ENSG00000184012, ENSG00000175538, ENSG00000211966, ENSG00000165905, ENSG00000163734, ENSG00000148702, ENSG00000169347 
PC_ 3 
Positive:  ENSG00000274422, ENSG00000270906, ENSG00000124107, ENSG00000160183, ENSG00000196091, ENSG00000145864, ENSG00000205922, ENSG00000230387, ENSG00000157502, ENSG00000029534 
	   ENSG00000133433, ENSG00000270909, ENSG00000204019, ENSG00000196436, ENSG00000137558, ENSG00000126709, ENSG00000235020, ENSG00000012223, ENSG00000247627, ENSG00000232721 
	   ENSG00000270154, ENSG00000137959, ENSG00000185290, ENSG00000144644, ENSG00000198744, ENSG00000089327, ENSG00000129451, ENSG00000279304, ENSG00000094755, ENSG00000136881 
Negative:  ENSG00000117983, ENSG00000187210, ENSG00000107807, ENSG00000036473, ENSG00000153823, ENSG00000100889, ENSG00000175344, ENSG00000118513, ENSG00000133477, ENSG00000164237 
	   ENSG00000115255, ENSG00000099617, ENSG00000278535, ENSG00000263429, ENSG00000166920, ENSG00000169715, ENSG00000198576, ENSG00000116771, ENSG00000125144, ENSG00000156966 
	   ENSG00000112494, ENSG00000161267, ENSG00000118322, ENSG00000224826, ENSG00000135097, ENSG00000116299, ENSG00000138823, ENSG00000124253, ENSG00000162482, ENSG00000178035 
PC_ 4 
Positive:  ENSG00000232216, ENSG00000064651, ENSG00000160182, ENSG00000241755, ENSG00000115386, ENSG00000211950, ENSG00000114248, ENSG00000143297, ENSG00000211893, ENSG00000275395 
	   ENSG00000105523, ENSG00000171747, ENSG00000211639, ENSG00000253691, ENSG00000254157, ENSG00000198099, ENSG00000211959, ENSG00000163618, ENSG00000131620, ENSG00000182938 
	   ENSG00000211938, ENSG00000271178, ENSG00000163751, ENSG00000211946, ENSG00000132465, ENSG00000099834, ENSG00000198910, ENSG00000260048, ENSG00000211666, ENSG00000112297 
Negative:  ENSG00000215030, ENSG00000069535, ENSG00000164070, ENSG00000003096, ENSG00000197172, ENSG00000236283, ENSG00000163032, ENSG00000258655, ENSG00000254471, ENSG00000261159 
	   ENSG00000196482, ENSG00000267924, ENSG00000274150, ENSG00000229835, ENSG00000186094, ENSG00000182263, ENSG00000198681, ENSG00000119782, ENSG00000185053, ENSG00000178568 
	   ENSG00000221867, ENSG00000242741, ENSG00000156284, ENSG00000156689, ENSG00000154162, ENSG00000178690, ENSG00000121388, ENSG00000281655, ENSG00000127074, ENSG00000205426 
PC_ 5 
Positive:  ENSG00000088882, ENSG00000113083, ENSG00000095752, ENSG00000154096, ENSG00000129988, ENSG00000106366, ENSG00000133048, ENSG00000170323, ENSG00000149968, ENSG00000181092 
	   ENSG00000148848, ENSG00000133488, ENSG00000166819, ENSG00000081041, ENSG00000143320, ENSG00000188257, ENSG00000214548, ENSG00000108342, ENSG00000176194, ENSG00000145536 
	   ENSG00000128510, ENSG00000257017, ENSG00000116690, ENSG00000183072, ENSG00000109705, ENSG00000187288, ENSG00000163394, ENSG00000182585, ENSG00000230615, ENSG00000173432 
Negative:  ENSG00000181617, ENSG00000174944, ENSG00000117322, ENSG00000249599, ENSG00000164176, ENSG00000249082, ENSG00000159307, ENSG00000129451, ENSG00000130222, ENSG00000156234 
	   ENSG00000262319, ENSG00000278928, ENSG00000221112, ENSG00000166509, ENSG00000167656, ENSG00000121769, ENSG00000105369, ENSG00000171885, ENSG00000163884, ENSG00000230778 
	   ENSG00000172987, ENSG00000133454, ENSG00000073067, ENSG00000103175, ENSG00000164764, ENSG00000138100, ENSG00000229314, ENSG00000156738, ENSG00000077943, ENSG00000236466 
Calculating cluster EBV
Calculating cluster GS
Warning: No DE genes identified
Final groups for plot: 3 -> Diffuse, Intestinal, Mixed
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Warning: Removed 6 rows containing missing values or values outside the scale range
(`geom_point()`).
Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-')
Using Seurat v5+ workflow
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix

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Finding variable features for layer counts
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Warning in svd.function(A = t(x = object), nv = npcs, ...) :
  You're computing too large a percentage of total singular values, use a standard svd instead.
PC_ 1 
Positive:  DMPK, NEGR1, MYLK, CSPG4, CNN1, FOXP2, CACNA1H, DNAJB5, PGM5, JPH2 
	   LMOD1, DACT3, ASB2, CAV1, SPEG, MTURN, FENDRR, RBPMS2, SYNM, RP11-554A11.5 
	   PRICKLE2, TSPAN18, SORBS1, FBXL22, CAP2, EML1, NPTXR, FERMT2, ACTG2, ANGPTL1 
Negative:  TSPAN13, BMP2, MAL2, CDC6, SPINT2, C12orf75, BAIAP2L1, SPINT1, ATP2C1, KCNK1 
	   UNC5CL, SLC9A7, MANEAL, CDH1, NFE2L3, HN1, SLCO4A1, LSR, STIL, LRRC16A 
	   RASSF7, CLDN4, SPINK1, CDCP1, HELZ2, RIPK4, CTSH, ETV7, PLS1, BRI3BP 
PC_ 2 
Positive:  IGHV5-51, IGHV3-23, FAM46C, IGLV3-21, IGHV3-21, IGHV1-46, IGKV3-20, IGHV4-34, CTSW, IGHV3-30 
	   IGLV3-1, IGLC2, IGLV2-11, IGHJ3, IGHV3-74, IGLL5, IGLV1-44, IGKV3D-11, IGKV3-15, IGHV3OR16-8 
	   IGKV3-7, PIM2, IGHV3-7, IGHV1-17, IGHV3-72, IGLV7-46, SPAG4, IGHV1-18, IGKV3D-20, IGHG2 
Negative:  KLK11, SNORD39, ILDR1, AKR1C2, MTND4P24, GJB5, DSG3, TRIM29, FGFBP1, AKR1C1 
	   MUC3A, AC069213.1, GJB4, FUT3, CLDN10-AS1, ANXA8L1, NPC1L1, SBSN, ANXA8, KRT17 
	   SPRR1B, NPY6R, CALML3, PDZK1, SPRR2A, RP11-223C24.2, SERPINE3, SPRR2D, KRT6A, SPRR2E 
PC_ 3 
Positive:  NCAM1, GLB1L2, TRPM5, KLHL13, KIAA1324, HEPACAM2, GAMT, SLC2A10, C15orf48, ARHGAP5-AS1 
	   AP000439.3, RNA5-8SP6, 5-8S-rRNA, NMU, GC, FKBP1B, RPS3AP5, KRT81, PTPN18, LINC00675 
	   SLC43A3, RGS13, FBP1, FOXI1, AVIL, APOH, RASSF10, RP11-778D9.4, CDH12, GLYATL2 
Negative:  ERAP2, CAPN8, CYP2C18, ONECUT3, IGHV4-39, GAL3ST1, GJB1, IGKV2-26, PLEKHG4, BLACAT1 
	   MIR4537, ANKRD36BP2, LEMD1, KLHDC7A, FOXA3, LAX1, SLC6A14, SYT13, IGHG4, IGKV5-2 
	   IGKV2D-24, IGHV3-64, IGHJ3P, IGKV1-16, LAMA3, IGKV2-30, APOBEC3B, IGLC3, RIN1, IGLJ3 
PC_ 4 
Positive:  B3GALT5, CES2, HTR1D, GAL3ST2, SULT1B1, ANPEP, AL901608.1, SI, CLDN15, ALDOB 
	   CHP2, PLAC8, TMEM150B, GPA33, MOGAT2, NAT2, CYP3A4, RP11-102C16.3, HMGA1P5, KCNJ3 
	   TUBAL3, MT1H, C10orf99, AC000111.6, PPP1R14D, ATP10B, CDX1, NOS2, B4GALNT2, CDX2 
Negative:  RP11-110G21.2, RNU4-62P, RNA5SP498, RNU6-758P, RNU4-40P, RNU6-1016P, RNU6-37P, RNY4P34, snoU13, MIR126 
	   RNU6-437P, MT-TY, RNU7-45P, RNU7-41P, RNU6-194P, RNU6-130P, RP11-475J5.6, CT83, RNU4-80P, KRT7 
	   RNU6-530P, RNA5SP84, MIR6801, RNU6-937P, MTND6P3, RNA5SP92, MIR5690, MIR199B, RNA5SP367, RNU6-321P 
PC_ 5 
Positive:  GABRP, SERPINB2, AC016735.2, IGLV1-41, IGHV3-38, RSAD2, IGKV2-29, IGKV1D-13, CTD-3018O17.5, IGKV1OR2-6 
	   IGKV1-13, MIR4316, RP11-412H8.2, CALB1, OASL, IGHV3-6, ANXA10, HRASLS2, IGKV6-21, BACE2 
	   IGHV3-35, RP11-457P14.6, DLGAP1-AS5, HOXC10, IGHV1OR16-1, MIR6731, IGHD4-17, CEACAM7, RASAL1, MIR664A 
Negative:  MIR559, TMEM82, ODAM, REG3A, DEFA6, PGA5, RNU7-14P, RNU7-97P, ATP4B, PGA3 
	   ATP4A, DEFA5, RP11-345K20.2, FAM3D, IGHD5-24, RPSAP8, RNU6-322P, RP1-68D18.4, RP11-789C1.2, BTNL8 
	   AADAC, SCGN, FOSB, APOLD1, SNORD116-12, SLC10A2, RNU6-14P, PRODH, RP11-64D22.5, RNU1-80P 
Calculating cluster Mixed
Calculating cluster Diffuse
Calculating cluster Intestinal
Final groups for plot: 3 -> Diffuse, Intestinal, Mixed
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Warning: Removed 120 rows containing missing values or values outside the scale range
(`geom_point()`).
Final groups for plot: 3 -> Diffuse, Intestinal, Mixed
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Warning: Removed 120 rows containing missing values or values outside the scale range
(`geom_point()`).
Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-')
Using Seurat v5+ workflow
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix

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Finding variable features for layer counts
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Warning in svd.function(A = t(x = object), nv = npcs, ...) :
  You're computing too large a percentage of total singular values, use a standard svd instead.
PC_ 1 
Positive:  DMPK, NEGR1, MYLK, CSPG4, CNN1, FOXP2, CACNA1H, DNAJB5, PGM5, JPH2 
	   LMOD1, DACT3, ASB2, CAV1, SPEG, MTURN, FENDRR, RBPMS2, SYNM, RP11-554A11.5 
	   PRICKLE2, TSPAN18, SORBS1, FBXL22, CAP2, EML1, NPTXR, FERMT2, ACTG2, ANGPTL1 
Negative:  TSPAN13, BMP2, MAL2, CDC6, SPINT2, C12orf75, BAIAP2L1, SPINT1, ATP2C1, KCNK1 
	   UNC5CL, SLC9A7, MANEAL, CDH1, NFE2L3, HN1, SLCO4A1, LSR, STIL, LRRC16A 
	   RASSF7, CLDN4, SPINK1, CDCP1, HELZ2, RIPK4, CTSH, ETV7, PLS1, BRI3BP 
PC_ 2 
Positive:  IGHV5-51, IGHV3-23, FAM46C, IGLV3-21, IGHV3-21, IGHV1-46, IGKV3-20, IGHV4-34, CTSW, IGHV3-30 
	   IGLV3-1, IGLC2, IGLV2-11, IGHJ3, IGHV3-74, IGLL5, IGLV1-44, IGKV3D-11, IGKV3-15, IGHV3OR16-8 
	   IGKV3-7, PIM2, IGHV3-7, IGHV1-17, IGHV3-72, IGLV7-46, SPAG4, IGHV1-18, IGKV3D-20, IGHG2 
Negative:  KLK11, SNORD39, ILDR1, AKR1C2, MTND4P24, GJB5, DSG3, TRIM29, FGFBP1, AKR1C1 
	   MUC3A, AC069213.1, GJB4, FUT3, CLDN10-AS1, ANXA8L1, NPC1L1, SBSN, ANXA8, KRT17 
	   SPRR1B, NPY6R, CALML3, PDZK1, SPRR2A, RP11-223C24.2, SERPINE3, SPRR2D, KRT6A, SPRR2E 
PC_ 3 
Positive:  NCAM1, GLB1L2, TRPM5, KLHL13, KIAA1324, HEPACAM2, GAMT, SLC2A10, C15orf48, ARHGAP5-AS1 
	   AP000439.3, RNA5-8SP6, 5-8S-rRNA, NMU, GC, FKBP1B, RPS3AP5, KRT81, PTPN18, LINC00675 
	   SLC43A3, RGS13, FBP1, FOXI1, AVIL, APOH, RASSF10, RP11-778D9.4, CDH12, GLYATL2 
Negative:  ERAP2, CAPN8, CYP2C18, ONECUT3, IGHV4-39, GAL3ST1, GJB1, IGKV2-26, PLEKHG4, BLACAT1 
	   MIR4537, ANKRD36BP2, LEMD1, KLHDC7A, FOXA3, LAX1, SLC6A14, SYT13, IGHG4, IGKV5-2 
	   IGKV2D-24, IGHV3-64, IGHJ3P, IGKV1-16, LAMA3, IGKV2-30, APOBEC3B, IGLC3, RIN1, IGLJ3 
PC_ 4 
Positive:  B3GALT5, CES2, HTR1D, GAL3ST2, SULT1B1, ANPEP, AL901608.1, SI, CLDN15, ALDOB 
	   CHP2, PLAC8, TMEM150B, GPA33, MOGAT2, NAT2, CYP3A4, RP11-102C16.3, HMGA1P5, KCNJ3 
	   TUBAL3, MT1H, C10orf99, AC000111.6, PPP1R14D, ATP10B, CDX1, NOS2, B4GALNT2, CDX2 
Negative:  RP11-110G21.2, RNU4-62P, RNA5SP498, RNU6-758P, RNU4-40P, RNU6-1016P, RNU6-37P, RNY4P34, snoU13, MIR126 
	   RNU6-437P, MT-TY, RNU7-45P, RNU7-41P, RNU6-194P, RNU6-130P, RP11-475J5.6, CT83, RNU4-80P, KRT7 
	   RNU6-530P, RNA5SP84, MIR6801, RNU6-937P, MTND6P3, RNA5SP92, MIR5690, MIR199B, RNA5SP367, RNU6-321P 
PC_ 5 
Positive:  GABRP, SERPINB2, AC016735.2, IGLV1-41, IGHV3-38, RSAD2, IGKV2-29, IGKV1D-13, CTD-3018O17.5, IGKV1OR2-6 
	   IGKV1-13, MIR4316, RP11-412H8.2, CALB1, OASL, IGHV3-6, ANXA10, HRASLS2, IGKV6-21, BACE2 
	   IGHV3-35, RP11-457P14.6, DLGAP1-AS5, HOXC10, IGHV1OR16-1, MIR6731, IGHD4-17, CEACAM7, RASAL1, MIR664A 
Negative:  MIR559, TMEM82, ODAM, REG3A, DEFA6, PGA5, RNU7-14P, RNU7-97P, ATP4B, PGA3 
	   ATP4A, DEFA5, RP11-345K20.2, FAM3D, IGHD5-24, RPSAP8, RNU6-322P, RP1-68D18.4, RP11-789C1.2, BTNL8 
	   AADAC, SCGN, FOSB, APOLD1, SNORD116-12, SLC10A2, RNU6-14P, PRODH, RP11-64D22.5, RNU1-80P 
Calculating cluster Mixed
Calculating cluster Diffuse
Calculating cluster Intestinal
Final groups for plot: 3 -> Diffuse, Intestinal, Mixed
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Warning: Removed 120 rows containing missing values or values outside the scale range
(`geom_point()`).
Final groups for plot: 3 -> Diffuse, Intestinal, Mixed
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Warning: Removed 120 rows containing missing values or values outside the scale range
(`geom_point()`).
>>>=== count to TPM...
>>>--- Using variables (anno_grch38) and gene lengths (eff_length)  built into the IOBR package to perform TPM transformation
>>>--- The gene lengths (eff_length) was estimated by function `getGeneLengthAndGCContent` from EDASeq package with default parameters at 2023-02-10
Warning in count2tpm(countMat = eset, idType = id_type, source = "local") :
  >>>--- Omit 3985 genes of which length is not available !
LR signature genes found in data set: 628/644 (97.5%)
Ligand-Receptor pair weights computed 

Warning in dir.create(folder_name) :
  cannot create dir 'Mutation_Results_20260303_073921', reason 'Permission denied'
Warning in dir.create(file_name) :
  cannot create dir 'Mutation_Results_20260303_073921', reason 'Permission denied'
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/srv/shiny-server/IOBRportal/Mutation_Results_20260303_073921/1-cuzickTest-test-relevant-mutations.csv': No such file or directory
Warning in dir.create(folder_name) :
  cannot create dir 'Mutation_Results_20260303_073955', reason 'Permission denied'
Warning in dir.create(file_name) :
  cannot create dir 'Mutation_Results_20260303_073955', reason 'Permission denied'
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/srv/shiny-server/IOBRportal/Mutation_Results_20260303_073955/1-cuzickTest-test-relevant-mutations.csv': No such file or directory
Warning in dir.create(folder_name) :
  cannot create dir 'Mutation_Results_20260303_074505', reason 'Permission denied'
Warning in dir.create(file_name) :
  cannot create dir 'Mutation_Results_20260303_074505', reason 'Permission denied'
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/srv/shiny-server/IOBRportal/Mutation_Results_20260303_074505/1-cuzickTest-test-relevant-mutations.csv': No such file or directory
Warning in dir.create(folder_name) :
  cannot create dir 'Mutation_Results_20260303_075101', reason 'Permission denied'
Warning in dir.create(file_name) :
  cannot create dir 'Mutation_Results_20260303_075101', reason 'Permission denied'
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/srv/shiny-server/IOBRportal/Mutation_Results_20260303_075101/1-cuzickTest-test-relevant-mutations.csv': No such file or directory


Closed TCGA pool.
Closed OtherCohort pool.
Closed immunotherapy pool.
Closed cancercohort pool.
Closed TCGA pool.
Closed OtherCohort pool.
Closed immunotherapy pool.
Closed cancercohort pool.
Execution halted