##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:COTAN.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings COTAN_2.9.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/COTAN.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'COTAN/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'COTAN' version '2.9.5'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'COTAN' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
UniformClusters         235.53   1.30  236.00
CalculatingCOEX          79.82   0.90   79.80
HandlingClusterizations  55.28   1.14   55.27
HeatmapPlots             52.31   1.05   52.75
ParametersEstimations    43.17   0.89   44.09
GenesStatistics          15.73   0.23   15.72
COTAN_ObjectCreation     14.28   0.29   14.31
Conversions               8.77   0.14    8.90
RawDataCleaning           5.36   0.11    5.53
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'outputTestDatasetCreation.R'
  Running 'spelling.R'
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL COTAN
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'COTAN' ...
** this is package 'COTAN' version '2.9.5'
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (COTAN)

R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> # Creates the files to be reloaded by the tests for comparisons
> library(zeallot)
> 
> outputTestDatasetCreation <- function(testsDir = file.path("tests",
+                                                            "testthat")) {
+   utils::data("test.dataset", package = "COTAN")
+   options(parallelly.fork.enable = TRUE)
+ 
+   obj <- COTAN(raw = test.dataset)
+   obj <- initializeMetaDataset(obj, GEO = " ",
+                                sequencingMethod = "artificial",
+                                sampleCondition = "test")
+ 
+   obj <- proceedToCoex(obj, cores = 6L, saveObj = FALSE)
+   #saveRDS(obj, file = file.path(testsDir,"temp.RDS"))
+ 
+   cells.names.test <- getCells(obj)[c(1L:10L, 591L:610L, 991L:1000L)]
+   genes.names.test <- getGenes(obj)[c(1L:10L, 291L:310L, 591L: 600L)]
+   saveRDS(cells.names.test, file.path(testsDir, "cells.names.test.RDS"))
+   saveRDS(genes.names.test, file.path(testsDir, "genes.names.test.RDS"))
+ 
+   dispersion.test <- getDispersion(obj)[genes.names.test]
+   saveRDS(dispersion.test, file.path(testsDir, "dispersion.test.RDS"))
+ 
+   raw.norm.test <- getNuNormData(obj)[genes.names.test, cells.names.test]
+   saveRDS(raw.norm.test, file.path(testsDir, "raw.norm.test.RDS"))
+ 
+   coex.test <- getGenesCoex(obj, genes = genes.names.test, zeroDiagonal = FALSE)
+   saveRDS(coex.test, file.path(testsDir, "coex.test.RDS"))
+ 
+   lambda.test <- getLambda(obj)[genes.names.test]
+   saveRDS(lambda.test, file.path(testsDir, "lambda.test.RDS"))
+ 
+   GDI.test <- calculateGDI(obj)
+   GDI.test <- GDI.test[genes.names.test, ]
+   saveRDS(GDI.test, file.path(testsDir, "GDI.test.RDS"))
+ 
+   nu.test <- getNu(obj)[cells.names.test]
+   saveRDS(nu.test, file.path(testsDir, "nu.test.RDS"))
+ 
+   pval.test <- calculatePValue(obj, geneSubsetCol = genes.names.test)
+   saveRDS(pval.test, file.path(testsDir, "pval.test.RDS"))
+ 
+   GDIThreshold <- 1.46
+   initialResolution <- 0.8
+   clusters <- cellsUniformClustering(obj, GDIThreshold = GDIThreshold,
+                                      initialResolution   = initialResolution,
+                                      cores = 6L, saveObj = FALSE)[["clusters"]]
+   saveRDS(clusters, file.path(testsDir, "clusters1.RDS"))
+ 
+   coexDF <- DEAOnClusters(obj, clusters = clusters)
+   obj <- addClusterization(obj, clName = "clusters",
+                            clusters = clusters, coexDF = coexDF)
+ 
+   saveRDS(coexDF[genes.names.test, ],
+           file.path(testsDir, "coex.test.cluster1.RDS"))
+ 
+   pvalDF <- pValueFromDEA(coexDF, getNumCells(obj), adjustmentMethod = "none")
+ 
+   saveRDS(pvalDF[genes.names.test, ],
+           file.path(testsDir, "pval.test.cluster1.RDS"))
+ 
+   c(mergedClusters, mCoexDF) %<-%
+     mergeUniformCellsClusters(objCOTAN = obj,
+                               clusters = NULL,
+                               GDIThreshold = GDIThreshold,
+                               cores = 6L,
+                               distance = "cosine",
+                               hclustMethod = "ward.D2",
+                               saveObj = FALSE)
+ 
+   saveRDS(mergedClusters[genes.names.test],
+           file.path(testsDir, "cluster_data_merged.RDS"))
+ }
> 
> proc.time()
   user  system elapsed 
   0.20    0.09    0.34 

R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> if (requireNamespace("spelling", quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
   0.17    0.03    0.26 

R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> Sys.setenv(R_TESTS = "")
> library(testthat)
> library(COTAN)
> test_check("COTAN")
Setting new log level to 4
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.9033203125 | max: 4.6796875 | % negative: 10
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.90468811988831
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00152707099914551
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0101699829101562
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.987221956253052
Total calculations elapsed time: 3.90360713005066
Calculate genes' COEX (legacy): DONE
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 5 genes batches
`dispersion` | min: 0.9033203125 | max: 4.6796875 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 7 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75595238095238 | median:  1.07174634176587 | mean:  1.07174634176587
Estimate `dispersion`/`nu`: START
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 1.0362548828125 | max: 4.60986328125 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0265938895089288 | median:  0.0144680038331048 | mean:  0.0144680038331048
`nu` mean: 1.69633192486233
Marginal errors | max: 1.95570586131367 | median 1.32068160171502 | mean: 1.33375826507259
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.058837890625 | max: 3.528076171875 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.416683423613994 | median:  0.239880630367975 | mean:  0.239880630367975
`nu` mean: 0.823197206753982
Marginal errors | max: 0.836359531101206 | median 0.703684202571891 | mean: 0.645537958989614
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.32879638671875 | max: 4.0302734375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.164237872898673 | median:  0.0955985184389135 | mean:  0.0955985184389135
`nu` mean: 1.06863935445976
Marginal errors | max: 0.259872988828242 | median 0.213703042752633 | mean: 0.197386407582083
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2294921875 | max: 3.8720703125 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.055185575120883 | median:  0.0319991762044448 | mean:  0.0319991762044448
`nu` mean: 0.976813601083562
Marginal errors | max: 0.0951586919577032 | median 0.079429703709466 | mean: 0.0724140148396648
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2637939453125 | max: 3.929443359375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0196211148938294 | median:  0.01138609597457 | mean:  0.01138609597457
`nu` mean: 1.00823501891926
Marginal errors | max: 0.0327747321002292 | median 0.0272104747849538 | mean: 0.0248963830312038
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.25177001953125 | max: 3.90966796875 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00670099066960717 | median:  0.00388888266671264 | mean:  0.00388888266671264
`nu` mean: 0.997187891997105
Marginal errors | max: 0.0114324509186883 | median 0.0094232649770607 | mean: 0.00863113610779571
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.25592041015625 | max: 3.91650390625 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00230093811689414 | median:  0.00132529122122246 | mean:  0.00132529122122246
`nu` mean: 1.00097564689567
Marginal errors | max: 0.00387133150664631 | median 0.0031091017608853 | mean: 0.00286071175800213
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2545166015625 | max: 3.914306640625 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.000837011646904529 | median:  0.000470837393363011 | mean:  0.000470837393363011
`nu` mean: 0.999633825746458
Marginal errors | max: 0.00122501723202006 | median 0.00102126435760308 | mean: 0.000943992659051318
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2550048828125 | max: 3.9150390625 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.000209227351122054 | median:  0.000122070312500028 | mean:  0.000122070312500028
`nu` mean: 1.00008715703862
Marginal errors | max: 0.000364602956581805 | median 0.000313956936819793 | mean: 0.000282899574318485
Estimate `dispersion`/`nu`: DONE
Estimate `dispersion`/`nu`: START
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.9033203125 | max: 4.6796875 | % negative: 10
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.13404893875122
Calculating genes' COEX normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.00130701065063477
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00522613525390625
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.976223945617676
Total calculations elapsed time: 4.11680603027344
Calculate genes' COEX (legacy): DONE
Calculate cells' COEX (legacy): START
Retrieving expected cells' contingency table
calculating NN.. done
calculating YN..NY..YY..t().. done
Expected cells' contingency table elapsed time: 3.06112790107727
Calculating cells' COEX normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.0018770694732666
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00444293022155762
Estimating cells' COEX
Calculate cells' COEX elapsed time: 0.919011116027832
Total calculations elapsed time: 3.98645901679993
Calculate cells' COEX (legacy): DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Running genes' selection: START
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Running genes' selection: START
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Running genes' selection: START
Selected 5 genes using HGDI selector
Running genes' selection: DONE
Running genes' selection: START
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Selected 5 genes using HVG_Seurat selector
Running genes' selection: DONE
Running genes' selection: START
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer data
Calculating gene means
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variance to mean ratios
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Running genes' selection: START
Given 5 genes as input
Running genes' selection: DONE
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Selected 8 genes using HGDI selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Selected 8 genes using HVG_Seurat selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Elaborating COEX Eigen Vectors - START
Elaborating COEX Eigen Vectors - DONE
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Elaborating COEX Eigen Vectors - START
Elaborating COEX Eigen Vectors - DONE
Elaborating Reduced dimensionality Data Matrix - DONE
Initializing `COTAN` meta-data
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate `dispersion`/`nu`: START
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.903564453125 | max: 4.679443359375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75719246031746 | median:  1.07229953342014 | mean:  1.07229953342014
`nu` mean: 1.68489292689732
Marginal errors | max: 1.73564890252257 | median 1.37996360874076 | mean: 1.32180348113228
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.0655517578125 | max: 3.5439453125 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.402649984216273 | median:  0.231868788425666 | mean:  0.231868788425666
`nu` mean: 0.829218804209393
Marginal errors | max: 0.80321315986594 | median 0.677497553540581 | mean: 0.619375430892821
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.3260498046875 | max: 4.026123046875 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.158004893526231 | median:  0.0919692884670312 | mean:  0.0919692884670312
`nu` mean: 1.0660356050592
Marginal errors | max: 0.250724014302326 | median 0.206232152124436 | mean: 0.190425623677198
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.23040771484375 | max: 3.8736572265625 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0532774732102337 | median:  0.0308837890624999 | mean:  0.0308837890624999
`nu` mean: 0.977606315852266
Marginal errors | max: 0.0916983669060123 | median 0.0765266929824948 | mean: 0.0697593208689684
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.26348876953125 | max: 3.928955078125 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0189966206463044 | median:  0.0110199320575908 | mean:  0.0110199320575908
`nu` mean: 1.00797668858871
Marginal errors | max: 0.0317151207459254 | median 0.0262702142278251 | mean: 0.0240886952086962
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2518310546875 | max: 3.9097900390625 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00670088501353994 | median:  0.00388888101583662 | mean:  0.00388888101583662
`nu` mean: 0.997187996002297
Marginal errors | max: 0.0113693316356223 | median 0.00939669372836249 | mean: 0.00860715734056932
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2559814453125 | max: 3.9166259765625 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00251007446998996 | median:  0.00144735987374958 | mean:  0.00144735987374958
`nu` mean: 1.00106271459624
Marginal errors | max: 0.00406746973787442 | median 0.00343393462175534 | mean: 0.00313496757119527
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.25445556640625 | max: 3.9140625 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.000837027590858019 | median:  0.000488281249999889 | mean:  0.000488281249999889
`nu` mean: 0.999651253659142
Marginal errors | max: 0.00143433714371533 | median 0.00116636244706747 | mean: 0.00109289166947839
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2550048828125 | max: 3.9150390625 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.000209227688885871 | median:  0.0001220703125 | mean:  0.0001220703125
`nu` mean: 1.00008715737639
Marginal errors | max: 0.000379524846207957 | median 0.000325685250686547 | mean: 0.000295532844332236
Estimate `dispersion`/`nu`: DONE
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.02051711082458
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000949859619140625
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00234818458557129
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.980227947235107
Total calculations elapsed time: 4.0040431022644
Calculate genes' COEX (legacy): DONE
Calculate cells' COEX (legacy): START
Retrieving expected cells' contingency table
calculating NN.. done
calculating YN..NY..YY..t().. done
Expected cells' contingency table elapsed time: 3.0378680229187
Calculating cells' COEX normalization factor
Calculate cells' normalization factor elapsed time: 0.00098109245300293
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00250506401062012
Estimating cells' COEX
Calculate cells' COEX elapsed time: 1.02288484573364
Total calculations elapsed time: 4.06423902511597
Calculate cells' COEX (legacy): DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Calculate genes' partial COEX: START
Retrieving expected genes' partial contingency table
calculating partial NN.. done
calculating partial NY..YN..YY.. done
Calculating genes' partial COEX normalization factor
Fraction of genes with very low expected contingency tables: 0.325
Retrieving observed genes' yes/yes partial contingency table
calculating partial YY.. done
Estimating genes' partial COEX
Calculate genes' partial COEX: DONE
Calculate cells' partial COEX: START
Retrieving expected cells' partial contingency table
calculating partial NN.. done
calculating partial YN..NY..YY.. done
Calculating cells' partial COEX normalization factor
Fraction of genes with very low expected contingency tables: 0
Retrieving observed cells' yes/yes partial contingency table
calculating partial YY.. done
Estimating cells' partial COEX
Calculate cells' partial COEX: DONE
Asked to drop 2 genes and 0 cells
Asked to drop 0 genes and 4 cells
Asked to drop 2 genes and 2 cells

Attaching package: 'rlang'

The following objects are masked from 'package:testthat':

    is_false, is_null, is_true

Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
calculating YY.. done
calculating YY.. done
calculating YN..NY..NN..t().. done
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
`dispersion` | min: 0.9033203125 | max: 4.6796875 | % negative: 10
calculating NN.. done
calculating NN.. done
calculating NY..YN..YY..t().. done
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.06685400009155
Calculating genes' COEX normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.0013120174407959
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00241994857788086
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.927975177764893
Total calculations elapsed time: 3.99856114387512
Calculate genes' COEX (legacy): DONE
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.95358800888062
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000905036926269531
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0023651123046875
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.02544188499451
Total calculations elapsed time: 3.98230004310608
Calculate genes' COEX (legacy): DONE
Calculate genes' partial COEX: START
Retrieving expected genes' partial contingency table
calculating partial NN.. done
calculating partial NY..YN..YY.. done
Calculating genes' partial COEX normalization factor
Fraction of genes with very low expected contingency tables: 0.1
Retrieving observed genes' yes/yes partial contingency table
calculating partial YY.. done
Estimating genes' partial COEX
Calculate genes' partial COEX: DONE
Calculate genes' partial COEX: START
Retrieving expected genes' partial contingency table
calculating partial NN.. done
calculating partial NY..YN..YY.. done
Calculating genes' partial COEX normalization factor
Fraction of genes with very low expected contingency tables: 0.4
Retrieving observed genes' yes/yes partial contingency table
calculating partial YY.. done
Estimating genes' partial COEX
Calculate genes' partial COEX: DONE
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
calculating YY.. done
calculating YY.. done
calculating NY..YN..NN..t().. done
Estimate `dispersion`/`nu`: START
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
`dispersion` | min: 0.903564453125 | max: 4.679443359375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75719246031746 | median:  1.07229953342014 | mean:  1.07229953342014
`nu` mean: 1.68489292689732
Marginal errors | max: 0.25535328937316 | median 0.0807577993228135 | mean: 0.101980750205762
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
`dispersion` | min: 1.037109375 | max: 4.6107177734375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0273438105507502 | median:  0.0148852611818011 | mean:  0.0148852611818011
`nu` mean: 1.69735147626627
Marginal errors | max: 0.00326864580272002 | median 0.00111524657842743 | mean: 0.00131556083122533
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
`dispersion` | min: 1.03887939453125 | max: 4.6097412109375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0 | median:  0 | mean:  0
`nu` mean: 1.69735147626627
Marginal errors | max: 7.56328383637594e-05 | median 1.72948087246994e-05 | mean: 2.99252342145451e-05
Estimate `dispersion`/`nu`: DONE
calculating NN.. done
calculating NN.. done
calculating YN..NY..YY..t().. done
Calculate cells' COEX (legacy): START
Retrieving expected cells' contingency table
calculating NN.. done
calculating YN..NY..YY..t().. done
Expected cells' contingency table elapsed time: 2.99870109558105
Calculating cells' COEX normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.00124406814575195
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00244283676147461
Estimating cells' COEX
Calculate cells' COEX elapsed time: 0.983517169952393
Total calculations elapsed time: 3.98590517044067
Calculate cells' COEX (legacy): DONE
Calculate cells' partial COEX: START
Retrieving expected cells' partial contingency table
calculating partial NN.. done
calculating partial YN..NY..YY.. done
Calculating cells' partial COEX normalization factor
Fraction of genes with very low expected contingency tables: 0
Retrieving observed cells' yes/yes partial contingency table
calculating partial YY.. done
Estimating cells' partial COEX
Calculate cells' partial COEX: DONE
Calculate cells' partial COEX: START
Retrieving expected cells' partial contingency table
calculating partial NN.. done
calculating partial YN..NY..YY.. done
Calculating cells' partial COEX normalization factor
Fraction of genes with very low expected contingency tables: 0
Retrieving observed cells' yes/yes partial contingency table
calculating partial YY.. done
Estimating cells' partial COEX
Calculate cells' partial COEX: DONE
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate `dispersion`/`nu`: START
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
`dispersion` | min: 0.903564453125 | max: 4.679443359375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75719246031746 | median:  1.07229953342014 | mean:  1.07229953342014
`nu` mean: 1.68489292689732
Marginal errors | max: 0.25535328937316 | median 0.0807577993228135 | mean: 0.101980750205762
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
`dispersion` | min: 1.037109375 | max: 4.6107177734375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0273438105507502 | median:  0.0148852611818011 | mean:  0.0148852611818011
`nu` mean: 1.69735147626627
Marginal errors | max: 0.00326864580272002 | median 0.00111524657842743 | mean: 0.00131556083122533
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
`dispersion` | min: 1.03887939453125 | max: 4.6097412109375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0 | median:  0 | mean:  0
`nu` mean: 1.69735147626627
Marginal errors | max: 7.56328383637594e-05 | median 1.72948087246994e-05 | mean: 2.99252342145451e-05
Estimate `dispersion`/`nu`: DONE
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.006756067276
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000941991806030273
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.002410888671875
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.02814793586731
Total calculations elapsed time: 4.03825688362122
Calculate genes' COEX (legacy): DONE
Calculating S: START
Calculating S: DONE
Calculating G: START
calculating YY.. done
calculating YN..NY..NN..t().. done
calculating NN.. done
calculating NY..YN..YY..t().. done
Estimating G
Calculating G: DONE
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values genome wide on columns and genome wide on rows
calculating PValues: DONE
Using G
Calculating G: START
calculating YY.. done
calculating YN..NY..NN..t().. done
calculating NN.. done
calculating NY..YN..YY..t().. done
Estimating G
Calculating G: DONE
calculating PValues: START
Get p-values on a set of genes on columns and on a set of genes on rows
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Calculate GDI dataframe: START
Using G
Calculating G: START
calculating YY.. done
calculating YN..NY..NN..t().. done
calculating NN.. done
calculating NY..YN..YY..t().. done
Estimating G
Calculating G: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Initializing `COTAN` meta-data
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 5.76655006408691
Cotan genes' COEX estimation started
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.61356616020203
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0160739421844482
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0643579959869385
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.06191492080688
Total calculations elapsed time: 4.7559130191803
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.72999286651611
Total elapsed time: 13.6228828430176
Initializing `COTAN` meta-data
Condition test
n cells 1200
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 5.46119904518127
Cotan genes' COEX estimation started
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.49706196784973
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0114030838012695
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0473790168762207
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.04168486595154
Total calculations elapsed time: 4.59752893447876
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.65152215957642
Total elapsed time: 13.1822400093079
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Condition test
n cells 1200
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 5.44779706001282
Cotan genes' COEX estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.56941699981689
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0150949954986572
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.059542179107666
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.04865384101868
Total calculations elapsed time: 4.69270801544189
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.7314829826355
Total elapsed time: 13.2566959857941
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Condition test
n cells 1200
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 5.43863701820374
Cotan genes' COEX estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.54238796234131
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0182080268859863
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0552828311920166
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.983756065368652
Total calculations elapsed time: 4.59963488578796
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.60728096961975
Total elapsed time: 13.072380065918
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Asked to drop 0 genes and 1160 cells
Cotan analysis functions started
Asked to drop 31 genes and 0 cells
Genes/cells selection done: dropped [31] genes and [0] cells
Working on [569] genes and [40] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.2119140625 | max: 85.5 | % negative: 62.2144112478032
Cotan genes' COEX estimation not requested
Total elapsed time: 6.04640817642212
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.09797215461731
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0153019428253174
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0129859447479248
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.03717088699341
Total calculations elapsed time: 4.16343092918396
Calculate genes' COEX (legacy): DONE
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.05243802070618
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0134060382843018
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0125930309295654
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.07287287712097
Total calculations elapsed time: 4.15130996704102
Calculate genes' COEX (legacy): DONE
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.14565396308899
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00948596000671387
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0097651481628418
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.02790689468384
Total calculations elapsed time: 4.19281196594238
Calculate genes' COEX (legacy): DONE
Hangling COTAN object with condition: test
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and on a set of genes on rows
calculating PValues: DONE
Handling genes type: G2
Handling genes type: G3
Initializing `COTAN` meta-data
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
PCA: START
Elaborating PCA - START
Elaborating PCA - DONE
PCA: DONE
Hierarchical clustering: START
Hierarchical clustering: DONE
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 5.4243369102478
Cotan genes' COEX estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.71206092834473
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0152690410614014
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.064586877822876
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.02703595161438
Total calculations elapsed time: 4.81895279884338
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.84460997581482
Total elapsed time: 16.8466229438782
Saving elaborated data locally at: F:\biocbuild\bbs-3.22-bioc\tmpdir\RtmpQNUxpM/test.cotan.RDS
Creating new clusterization: START
Elaborating Reduced dimensionality Data Matrix - START
Elaborating COEX Eigen Vectors - START
Elaborating COEX Eigen Vectors - DONE
Elaborating Reduced dimensionality Data Matrix - DONE
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1200
Number of edges: 37723

Running Louvain algorithm with multilevel refinement...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5827
Number of communities: 2
Elapsed time: 0 seconds
Number of clusters is too small. Reclustering at resolution higher than: 0.8
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1200
Number of edges: 37723

Running Louvain algorithm with multilevel refinement...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.3954
Number of communities: 5
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 1.3
Creating new clusterization: DONE
Creating cells' uniform clustering: START
In iteration 1 the number of cells to re-cluster is 1200 cells belonging to 0 clusters
Asked to drop no genes or cells
Creating new clusterization: START
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Selected 600 genes using HVG_Seurat selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Elaborating Reduced dimensionality Data Matrix - DONE
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1200
Number of edges: 55489

Running Louvain algorithm with multilevel refinement...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5973
Number of communities: 4
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 0.8
Creating new clusterization: DONE
Creating PDF UMAP in file:  F:\biocbuild\bbs-3.22-bioc\tmpdir\RtmpQNUxpM/test/reclustering/pdf_umap_1.pdf
UMAP plot
Calculating UMAP: START
02:23:27 UMAP embedding parameters a = 0.9922 b = 1.112
02:23:27 Read 1200 rows and found 40 numeric columns
02:23:27 Using Annoy for neighbor search, n_neighbors = 30
02:23:27 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
02:23:27 Writing NN index file to temp file F:\biocbuild\bbs-3.22-bioc\tmpdir\RtmpQNUxpM\file19b0c6e582992
02:23:27 Searching Annoy index using 1 thread, search_k = 3000
02:23:27 Annoy recall = 100%
02:23:28 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
02:23:30 Initializing from normalized Laplacian + noise (using RSpectra)
02:23:31 Commencing optimization for 500 epochs, with 42674 positive edges
02:23:31 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
02:23:35 Optimization finished
Calculating UMAP: DONE
UMAP plot
Calculating UMAP: START
02:23:36 UMAP embedding parameters a = 0.9922 b = 1.112
02:23:36 Read 1200 rows and found 40 numeric columns
02:23:36 Using Annoy for neighbor search, n_neighbors = 30
02:23:36 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
02:23:36 Writing NN index file to temp file F:\biocbuild\bbs-3.22-bioc\tmpdir\RtmpQNUxpM\file19b0c69442e40
02:23:36 Searching Annoy index using 1 thread, search_k = 3000
02:23:36 Annoy recall = 100%
02:23:37 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
02:23:39 Initializing from normalized Laplacian + noise (using RSpectra)
02:23:39 Commencing optimization for 500 epochs, with 42674 positive edges
02:23:39 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
02:23:44 Optimization finished
Calculating UMAP: DONE
* checking uniformity of cluster '0' of 4 clusters
Asked to drop 0 genes and 847 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [353] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.038818359375 | max: 11.109375 | % negative: 5
Only analysis elapsed time: 3.851891040802
Cotan genes' COEX estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.43920111656189
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0124390125274658
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.03830885887146
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.0699770450592
Total calculations elapsed time: 4.55992603302002
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.66462707519531
Total elapsed time: 11.5493791103363
Checking uniformity for the cluster '01_0000' with 353 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0000, with size 353, is uniform
Cluster 01_0000's shift to uniformity: -0.0160990564073067
class = SimpleGDIUniformityCheck, check.isCheckAbove = FALSE, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0.00833333333333333, check.thresholdRank = 0, check.quantileAtRatio = 1.44390094359269, check.quantileAtRank = NaN, isUniform = TRUE, clusterSize = 353
cluster 01_0000 is uniform

* checking uniformity of cluster '1' of 4 clusters
Asked to drop 0 genes and 879 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [321] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0501708984375 | max: 14.515625 | % negative: 8.5
Only analysis elapsed time: 3.83286118507385
Cotan genes' COEX estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.42822790145874
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0117790699005127
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0334129333496094
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.09928393363953
Total calculations elapsed time: 4.57270383834839
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.6035418510437
Total elapsed time: 11.6857168674469
Checking uniformity for the cluster '01_0001' with 321 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0001, with size 321, is uniform
Cluster 01_0001's shift to uniformity: -0.029501740796509
class = SimpleGDIUniformityCheck, check.isCheckAbove = FALSE, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0.005, check.thresholdRank = 0, check.quantileAtRatio = 1.43049825920349, check.quantileAtRank = NaN, isUniform = TRUE, clusterSize = 321
cluster 01_0001 is uniform

* checking uniformity of cluster '2' of 4 clusters
Asked to drop 0 genes and 905 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [295] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.054443359375 | max: 104 | % negative: 36.5
Only analysis elapsed time: 3.72623419761658
Cotan genes' COEX estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.48858904838562
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0155060291290283
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0226948261260986
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.02547597885132
Total calculations elapsed time: 4.55226588249207
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.60669493675232
Total elapsed time: 11.5339179039001
Checking uniformity for the cluster '01_0002' with 295 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0002, with size 295, is uniform
Cluster 01_0002's shift to uniformity: -0.0675248136510636
class = SimpleGDIUniformityCheck, check.isCheckAbove = FALSE, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0, check.thresholdRank = 0, check.quantileAtRatio = 1.39247518634894, check.quantileAtRank = NaN, isUniform = TRUE, clusterSize = 295
cluster 01_0002 is uniform

* checking uniformity of cluster '3' of 4 clusters
Asked to drop 0 genes and 969 cells
Cotan analysis functions started
Asked to drop 1 genes and 0 cells
Genes/cells selection done: dropped [1] genes and [0] cells
Working on [599] genes and [231] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0662841796875 | max: 82.5 | % negative: 33.889816360601
Only analysis elapsed time: 3.57071304321289
Cotan genes' COEX estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.26347613334656
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0123429298400879
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.018064022064209
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.05151104927063
Total calculations elapsed time: 4.34539413452148
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.46557903289795
Total elapsed time: 11.2726430892944
Checking uniformity for the cluster '01_0003' with 231 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0003, with size 231, is uniform
Cluster 01_0003's shift to uniformity: -0.0869783653733054
class = SimpleGDIUniformityCheck, check.isCheckAbove = FALSE, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0, check.thresholdRank = 0, check.quantileAtRatio = 1.37302163462669, check.quantileAtRank = NaN, isUniform = TRUE, clusterSize = 231
cluster 01_0003 is uniform


Found 4 uniform and  0 non-uniform clusters
Stopping: too few cells left to cluster
Unclustered cell left: 0
The final raw clusterization contains [ 4 ] different clusters: 01_0000, 01_0001, 01_0002, 01_0003
Differential Expression Analysis - START
* DEA on cluster '1' with 353 cells
* DEA on cluster '2' with 321 cells
* DEA on cluster '3' with 295 cells
* DEA on cluster '4' with 231 cells

Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1  ->  3, 2  ->  1, 3  ->  2, 4  ->  4
Creating cells' uniform clustering: DONE
Applied reordering to clusterization is:
1  ->  1, 2  ->  2, 3  ->  3, 4  ->  4
Asked to drop 0 genes and 905 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [295] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.054443359375 | max: 104 | % negative: 36.5
Only analysis elapsed time: 3.68963503837585
Cotan genes' COEX estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.49483895301819
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0164289474487305
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0235970020294189
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.07098603248596
Total calculations elapsed time: 4.6058509349823
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.71249794960022
Total elapsed time: 11.5450689792633
Checking uniformity for the cluster 'Cluster_2' with 295 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster Cluster_2, with size 295, is uniform
Cluster Cluster_2's shift to uniformity: -0.00560790972802017
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0416666666666667, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.29139209027198, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.035, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.34700400911787, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00833333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.39247518634894, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 5, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.4279762218014, isUniform = TRUE, clusterSize = 295
Differential Expression Analysis - START
* DEA on cluster '-1' with 50 cells
* DEA on cluster '1' with 321 cells
* DEA on cluster '2' with 245 cells
* DEA on cluster '3' with 353 cells
* DEA on cluster '4' with 231 cells

Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1  ->  2, 2  ->  1, 3  ->  4, 4  ->  3, -1  ->  -1
Applied reordering to clusterization is:
1  ->  2, 2  ->  3, 3  ->  1, 4  ->  4, -1  ->  -1
Creating cells' uniform clustering: START
In iteration 1 the number of cells to re-cluster is 1200 cells belonging to 0 clusters
Asked to drop no genes or cells
Creating new clusterization: START
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Included 186 genes with GDI below 1.3
Selected 600 genes using HGDI selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Elaborating Reduced dimensionality Data Matrix - DONE
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1200
Number of edges: 55489

Running Louvain algorithm with multilevel refinement...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5973
Number of communities: 4
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 0.8
Creating new clusterization: DONE
Using passed in clusterization
Creating PDF UMAP in file:  F:\biocbuild\bbs-3.22-bioc\tmpdir\RtmpQNUxpM/test/reclustering/pdf_umap_1.pdf
UMAP plot
Calculating UMAP: START
02:25:29 UMAP embedding parameters a = 0.9922 b = 1.112
02:25:29 Read 1200 rows and found 40 numeric columns
02:25:29 Using Annoy for neighbor search, n_neighbors = 30
02:25:29 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
02:25:29 Writing NN index file to temp file F:\biocbuild\bbs-3.22-bioc\tmpdir\RtmpQNUxpM\file19b0c7b416065
02:25:29 Searching Annoy index using 1 thread, search_k = 3000
02:25:29 Annoy recall = 100%
02:25:31 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
02:25:33 Initializing from normalized Laplacian + noise (using RSpectra)
02:25:33 Commencing optimization for 500 epochs, with 42644 positive edges
02:25:33 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
02:25:38 Optimization finished
Calculating UMAP: DONE
UMAP plot
Calculating UMAP: START
02:25:38 UMAP embedding parameters a = 0.9922 b = 1.112
02:25:38 Read 1200 rows and found 40 numeric columns
02:25:38 Using Annoy for neighbor search, n_neighbors = 30
02:25:38 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
02:25:38 Writing NN index file to temp file F:\biocbuild\bbs-3.22-bioc\tmpdir\RtmpQNUxpM\file19b0c3a57f2a
02:25:38 Searching Annoy index using 1 thread, search_k = 3000
02:25:39 Annoy recall = 100%
02:25:40 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
02:25:42 Initializing from normalized Laplacian + noise (using RSpectra)
02:25:42 Commencing optimization for 500 epochs, with 42644 positive edges
02:25:42 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
02:25:47 Optimization finished
Calculating UMAP: DONE
* checking uniformity of cluster '1' of 2 clusters
Asked to drop 0 genes and 600 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [600] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0386962890625 | max: 19.40625 | % negative: 6.5
Only analysis elapsed time: 4.40503692626953
Cotan genes' COEX estimation started
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.50515007972717
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0121350288391113
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0366129875183105
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.03639006614685
Total calculations elapsed time: 4.59028816223145
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.70845293998718
Total elapsed time: 12.261528968811
Checking uniformity for the cluster '01_0001' with 600 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0001, with size 600, is uniform
Cluster 01_0001's shift to uniformity: -0.012256083873327
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0383333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.38474391612667, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.035, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42418110276821, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00666666666666667, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.45338035249413, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 4, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.51521594648007, isUniform = TRUE, clusterSize = 600
cluster 01_0001 is uniform

* checking uniformity of cluster '2' of 2 clusters
Asked to drop 0 genes and 600 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [600] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.032958984375 | max: 10.0859375 | % negative: 3.66666666666667
Only analysis elapsed time: 4.45547389984131
Cotan genes' COEX estimation started
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.66625118255615
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.015056848526001
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0523860454559326
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.0981559753418
Total calculations elapsed time: 4.83185005187988
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.93986105918884
Total elapsed time: 12.6172449588776
Checking uniformity for the cluster '01_0002' with 600 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0002, with size 600, is uniform
Cluster 01_0002's shift to uniformity: -0.0203445505533575
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0366666666666667, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.37665544944664, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.0316666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42305229982216, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00333333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.43783135828069, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 2, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.50182972335853, isUniform = TRUE, clusterSize = 600
cluster 01_0002 is uniform


Found 2 uniform and  0 non-uniform clusters
Stopping: too few cells left to cluster
Unclustered cell left: 0
The final raw clusterization contains [ 2 ] different clusters: 01_0001, 01_0002
Differential Expression Analysis - START
* DEA on cluster '1' with 600 cells
* DEA on cluster '2' with 600 cells

Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1  ->  1, 2  ->  2
Creating cells' uniform clustering: DONE
findClustersMarkers - START
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
* Analysis of cluster: '3'
* Analysis of cluster: '4'

Log Fold Change Analysis - DONE
findClustersMarkers - DONE
findClustersMarkers - START
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
* Analysis of cluster: '3'
* Analysis of cluster: '4'

Log Fold Change Analysis - DONE
findClustersMarkers - DONE
findClustersMarkers - START
Differential Expression Analysis - START
* DEA on cluster '1' with 321 cells
* DEA on cluster '2' with 295 cells
* DEA on cluster '3' with 353 cells
* DEA on cluster '4' with 231 cells

Differential Expression Analysis - DONE
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
* Analysis of cluster: '3'
* Analysis of cluster: '4'

Log Fold Change Analysis - DONE
findClustersMarkers - DONE
[1] "Tested cluster: 1"
Asked to drop 0 genes and 879 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [321] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0501708984375 | max: 14.515625 | % negative: 8.5
Only analysis elapsed time: 3.73158502578735
Cotan genes' COEX estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.36215496063232
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0115392208099365
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0350608825683594
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.14309406280518
Total calculations elapsed time: 4.5518491268158
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.68751382827759
Total elapsed time: 11.5515949726105
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
[1] "Tested cluster: 4"
Asked to drop 0 genes and 969 cells
Cotan analysis functions started
Asked to drop 1 genes and 0 cells
Genes/cells selection done: dropped [1] genes and [0] cells
Working on [599] genes and [231] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0662841796875 | max: 82.5 | % negative: 33.889816360601
Only analysis elapsed time: 3.63203001022339
Cotan genes' COEX estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.44042587280273
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0153300762176514
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0228829383850098
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.07628011703491
Total calculations elapsed time: 4.55491900444031
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.66608810424805
Total elapsed time: 11.4252381324768
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Initializing `COTAN` meta-data
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Cotan genes' COEX estimation not requested
Total elapsed time: 9.18655705451965
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
PC_ 1 
Positive:  g-000558, g-000570, g-000499, g-000504, g-000546, g-000506, g-000503, g-000517, g-000596, g-000528 
	   g-000527, g-000580, g-000592, g-000578, g-000509, g-000488, g-000555, g-000577, g-000534, g-000583 
	   g-000598, g-000535, g-000512, g-000554, g-000519, g-000525, g-000548, g-000544, g-000502, g-000541 
Negative:  g-000133, g-000007, g-000074, g-000141, g-000057, g-000235, g-000170, g-000019, g-000195, g-000140 
	   g-000183, g-000031, g-000046, g-000178, g-000177, g-000161, g-000157, g-000139, g-000011, g-000135 
	   g-000125, g-000208, g-000061, g-000085, g-000204, g-000104, g-000237, g-000004, g-000038, g-000128 
PC_ 2 
Positive:  g-000584, g-000583, g-000544, g-000519, g-000575, g-000516, g-000585, g-000486, g-000489, g-000539 
	   g-000484, g-000502, g-000523, g-000595, g-000305, g-000574, g-000599, g-000589, g-000509, g-000538 
	   g-000526, g-000551, g-000579, g-000590, g-000445, g-000556, g-000543, g-000501, g-000504, g-000570 
Negative:  g-000039, g-000050, g-000175, g-000078, g-000116, g-000189, g-000135, g-000047, g-000072, g-000087 
	   g-000063, g-000235, g-000066, g-000109, g-000018, g-000074, g-000231, g-000136, g-000034, g-000207 
	   g-000128, g-000167, g-000171, g-000049, g-000182, g-000013, g-000054, g-000062, g-000240, g-000158 
PC_ 3 
Positive:  g-000015, g-000575, g-000483, g-000316, g-000025, g-000364, g-000050, g-000278, g-000443, g-000360 
	   g-000332, g-000124, g-000212, g-000387, g-000536, g-000252, g-000251, g-000321, g-000501, g-000470 
	   g-000582, g-000106, g-000455, g-000368, g-000081, g-000104, g-000437, g-000288, g-000386, g-000317 
Negative:  g-000211, g-000337, g-000129, g-000185, g-000397, g-000403, g-000253, g-000098, g-000390, g-000303 
	   g-000052, g-000088, g-000463, g-000468, g-000236, g-000209, g-000005, g-000375, g-000342, g-000262 
	   g-000388, g-000091, g-000413, g-000285, g-000003, g-000095, g-000142, g-000205, g-000432, g-000241 
PC_ 4 
Positive:  g-000334, g-000398, g-000292, g-000095, g-000097, g-000202, g-000382, g-000195, g-000007, g-000079 
	   g-000086, g-000240, g-000263, g-000317, g-000576, g-000557, g-000160, g-000154, g-000214, g-000228 
	   g-000313, g-000053, g-000524, g-000374, g-000568, g-000188, g-000358, g-000528, g-000362, g-000150 
Negative:  g-000379, g-000193, g-000212, g-000434, g-000593, g-000513, g-000177, g-000223, g-000069, g-000131 
	   g-000162, g-000345, g-000462, g-000484, g-000448, g-000229, g-000365, g-000302, g-000010, g-000366 
	   g-000051, g-000535, g-000269, g-000270, g-000155, g-000529, g-000373, g-000008, g-000393, g-000306 
PC_ 5 
Positive:  g-000518, g-000108, g-000186, g-000170, g-000401, g-000337, g-000047, g-000599, g-000432, g-000578 
	   g-000042, g-000065, g-000493, g-000261, g-000533, g-000256, g-000560, g-000596, g-000368, g-000381 
	   g-000535, g-000338, g-000215, g-000159, g-000365, g-000234, g-000173, g-000387, g-000225, g-000272 
Negative:  g-000451, g-000339, g-000295, g-000328, g-000544, g-000061, g-000227, g-000391, g-000556, g-000237 
	   g-000067, g-000165, g-000449, g-000591, g-000087, g-000129, g-000197, g-000203, g-000487, g-000505 
	   g-000333, g-000029, g-000271, g-000064, g-000583, g-000156, g-000448, g-000153, g-000526, g-000393 
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1200
Number of edges: 55940

Running Louvain algorithm with multilevel refinement...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5920
Number of communities: 4
Elapsed time: 0 seconds
Clusterizations found: RNA_snn_res.0.8, seurat_clusters
Conditions found: orig.ident
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Cotan genes' COEX estimation not requested
Total elapsed time: 9.43067717552185
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 5.86090183258057
Cotan genes' COEX estimation started
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.88241410255432
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0154409408569336
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0625021457672119
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.14499592781067
Total calculations elapsed time: 5.10535311698914
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 6.19193315505981
Total elapsed time: 14.2816410064697
Calculating gene co-expression space - START
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
calculating PValues: DONE
Number of selected secondary markers: 6
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 6
Number of rows (U set): 60
Calculating gene co-expression space - DONE
Calculating gene co-expression space - START
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
calculating PValues: DONE
Number of selected secondary markers: 109
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 109
Number of rows (U set): 60
Calculating gene co-expression space - DONE
Establishing gene clusters - START
Calculating gene co-expression space - START
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
calculating PValues: DONE
Number of selected secondary markers: 109
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 109
Number of rows (U set): 60
Calculating gene co-expression space - DONE
Establishing gene clusters - DONE
Initializing `COTAN` meta-data
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Cotan genes' COEX estimation not requested
Total elapsed time: 9.43075203895569
Differential Expression Analysis - START
* DEA on cluster '1' with 353 cells
* DEA on cluster '2' with 221 cells
* DEA on cluster '3' with 315 cells
* DEA on cluster '4' with 311 cells

Differential Expression Analysis - DONE
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
* Analysis of cluster: '3'
* Analysis of cluster: '4'

Log Fold Change Analysis - DONE
clustersDeltaExpression - START
Handling cluster '1' with mean UDE 1.43530796540674
Handling cluster '2' with mean UDE 0.640931107489519
Handling cluster '3' with mean UDE 0.546546914955575
Handling cluster '4' with mean UDE 1.22034802329657
clustersDeltaExpression - DONE
In group G1 there are 3 detected over 3 genes
In group G2 there are 2 detected over 2 genes
In group G3 there are 5 detected over 5 genes
Merging cells' uniform clustering: START
The merge algorithm will use 2 passes
Start merging nearest clusters - the main threshold is: 1.297
Start merging nearest clusters: iteration 1
Differential Expression Analysis - START
* DEA on cluster '1' with 353 cells
* DEA on cluster '2' with 221 cells
* DEA on cluster '3' with 315 cells
* DEA on cluster '4' with 311 cells

Differential Expression Analysis - DONE
Updating check results for the 0 already tested pairs to align to new checker
2 new clusters pairs to be tested for merging:
c("1", "2") c("3", "4")
*1_2-merge
Asked to drop 0 genes and 626 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [574] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0340576171875 | max: 10.4375 | % negative: 4.33333333333333
Only analysis elapsed time: 4.5928328037262
Cotan genes' COEX estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.68881487846375
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0159890651702881
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0521240234375
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.15353798866272
Total calculations elapsed time: 4.91046595573425
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 6.01035904884338
Total elapsed time: 12.9281959533691
Checking uniformity for the cluster '1_2-merge' with 574 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 1_2-merge, with size 574, is not uniform
Cluster 1_2-merge's shift to uniformity: 0.0820221369127518
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.326666666666667, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.37902213691275, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.28, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.41724738266283, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.0333333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.42971854140312, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 20, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.5067755752749, isUniform = FALSE, clusterSize = 574
Clusters 1 and 2 cannot be merged
*3_4-merge
Asked to drop 0 genes and 574 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [626] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.03839111328125 | max: 17.40625 | % negative: 6.66666666666667
Only analysis elapsed time: 4.51609015464783
Cotan genes' COEX estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.66493010520935
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0157148838043213
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0460259914398193
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.15759015083313
Total calculations elapsed time: 4.88426113128662
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 6.04837894439697
Total elapsed time: 12.833664894104
Checking uniformity for the cluster '3_4-merge' with 626 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 3_4-merge, with size 626, is not uniform
Cluster 3_4-merge's shift to uniformity: 0.0914611744346074
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.248333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.38846117443461, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.218333333333333, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42066795244751, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.0366666666666667, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.45442688129939, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 22, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.52592182249635, isUniform = FALSE, clusterSize = 626
Clusters 3 and 4 cannot be merged
Finished the first batch - no merges were executed
Start merging nearest clusters: iteration 2
Differential Expression Analysis - START
* DEA on cluster '1' with 353 cells
* DEA on cluster '2' with 221 cells
* DEA on cluster '3' with 315 cells
* DEA on cluster '4' with 311 cells

Differential Expression Analysis - DONE
Updating check results for the 2 already tested pairs to align to new checker
2 new clusters pairs to be tested for merging:
c("2", "3") c("2", "4")
*2_3-merge
Asked to drop 0 genes and 664 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [536] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0390625 | max: 12.59375 | % negative: 9.16666666666667
Only analysis elapsed time: 4.14009809494019
Cotan genes' COEX estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.64449310302734
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0158989429473877
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0332729816436768
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.03738713264465
Total calculations elapsed time: 4.73105216026306
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.86048293113708
Total elapsed time: 12.2375719547272
Checking uniformity for the cluster '2_3-merge' with 536 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 2_3-merge, with size 536, is not uniform
Cluster 2_3-merge's shift to uniformity: 0.102213698003777
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.29, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.39921369800378, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.251666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.45276697088286, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.05, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.49016449535422, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 30, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.54477108741147, isUniform = FALSE, clusterSize = 536
Clusters 2 and 3 cannot be merged
*2_4-merge
Asked to drop 0 genes and 668 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [532] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.04754638671875 | max: 10.234375 | % negative: 5
Only analysis elapsed time: 4.37488102912903
Cotan genes' COEX estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.64051508903503
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0133810043334961
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.043895959854126
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.12081813812256
Total calculations elapsed time: 4.81861019134521
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.95900797843933
Total elapsed time: 12.5042719841003
Checking uniformity for the cluster '2_4-merge' with 532 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 2_4-merge, with size 532, is not uniform
Cluster 2_4-merge's shift to uniformity: 0.213129217682233
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.39, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.51012921768223, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.361666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.55599610798341, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.181666666666667, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.59088431608469, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 109, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.68475283375668, isUniform = FALSE, clusterSize = 532
Clusters 2 and 4 cannot be merged
No clusters will be merged
None of the remaining tested cluster pairs could be merged
Executed all merges for threshold 1.297 out of 4 checks
Start merging nearest clusters - the main threshold is: 1.397
Start merging nearest clusters: iteration 3
Differential Expression Analysis - START
* DEA on cluster '1' with 353 cells
* DEA on cluster '2' with 221 cells
* DEA on cluster '3' with 315 cells
* DEA on cluster '4' with 311 cells

Differential Expression Analysis - DONE
Updating check results for the 4 already tested pairs to align to new checker
2 new clusters pairs to be tested for merging:
c("1", "3") c("1", "4")
*1_3-merge
Asked to drop 0 genes and 532 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [668] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.046630859375 | max: 9.03515625 | % negative: 1.33333333333333
Only analysis elapsed time: 4.67769908905029
Cotan genes' COEX estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.61837005615234
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0114190578460693
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0401768684387207
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.90717601776123
Total calculations elapsed time: 4.57714200019836
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.48962593078613
Total elapsed time: 12.4155340194702
Checking uniformity for the cluster '1_3-merge' with 668 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 1_3-merge, with size 668, is not uniform
Cluster 1_3-merge's shift to uniformity: 0.177923707405303
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.33, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.5749237074053, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.31, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.6368755707341, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.128333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.65704996173771, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 77, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.68881338289977, isUniform = FALSE, clusterSize = 668
Clusters 1 and 3 cannot be merged
*1_4-merge
Asked to drop 0 genes and 536 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [664] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0164794921875 | max: 5.5595703125 | % negative: 0.166666666666667
Only analysis elapsed time: 4.55333709716797
Cotan genes' COEX estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.48227500915527
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.015437126159668
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0586519241333008
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.0403790473938
Total calculations elapsed time: 4.59674310684204
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.7459089756012
Total elapsed time: 12.2657289505005
Checking uniformity for the cluster '1_4-merge' with 664 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 1_4-merge, with size 664, is not uniform
Cluster 1_4-merge's shift to uniformity: 0.138277355686157
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.348333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.53527735568616, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.316666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.55951216335001, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.0983333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.59105696847609, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 59, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.64605433203111, isUniform = FALSE, clusterSize = 664
Clusters 1 and 4 cannot be merged
Clusters 2 and 1 will be merged
Clusters 3 and 4 will be merged
Executed 2 merges
Start merging nearest clusters: iteration 4
Differential Expression Analysis - START
* DEA on cluster '1_2-merge' with 574 cells
* DEA on cluster '3_4-merge' with 626 cells

Differential Expression Analysis - DONE
Updating check results for the 6 already tested pairs to align to new checker
1 new clusters pairs to be tested for merging:
c("1_2-merge", "3_4-merge")
*1_2-merge_3_4-merge-merge
Asked to drop no genes or cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 5.78579211235046
Cotan genes' COEX estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.86522507667542
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0135929584503174
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0592110157012939
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.09009408950806
Total calculations elapsed time: 5.02812314033508
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 6.09378790855408
Total elapsed time: 14.0655069351196
Checking uniformity for the cluster '1_2-merge_3_4-merge-merge' with 1200 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 1_2-merge_3_4-merge-merge, with size 1200, is not uniform
Cluster 1_2-merge_3_4-merge-merge's shift to uniformity: 0.173174985379327
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.415, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.57017498537933, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.388333333333333, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.61240081401504, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.15, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.64046660675367, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 90, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.66512085964758, isUniform = FALSE, clusterSize = 1200
Clusters 1_2-merge and 3_4-merge cannot be merged
No clusters will be merged
None of the remaining tested cluster pairs could be merged
Executed all merges for threshold 1.397 out of 7 checks
The final merged clusterization contains [2] different clusters: 1_2-merge, 3_4-merge
Differential Expression Analysis - START
* DEA on cluster '1' with 574 cells
* DEA on cluster '2' with 626 cells

Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1  ->  1, 2  ->  2
Merging cells' uniform clustering: DONE
Applied reordering to clusterization is:
1  ->  1, 2  ->  2
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'

Log Fold Change Analysis - DONE
Asked to drop 0 genes and 626 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [574] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0340576171875 | max: 10.4375 | % negative: 4.33333333333333
Only analysis elapsed time: 4.27484798431396
Cotan genes' COEX estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.52519607543945
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0164830684661865
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0532288551330566
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.973718166351318
Total calculations elapsed time: 4.56862616539001
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.6834659576416
Total elapsed time: 12.0979480743408
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Asked to drop 0 genes and 574 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [626] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.03839111328125 | max: 17.40625 | % negative: 6.66666666666667
Only analysis elapsed time: 4.48086905479431
Cotan genes' COEX estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet

Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.65757608413696
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0161399841308594
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0463049411773682
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.11613011360168
Total calculations elapsed time: 4.83615112304688
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 5.89681696891785
Total elapsed time: 12.6340119838715
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
[ FAIL 0 | WARN 45 | SKIP 0 | PASS 572 ]

[ FAIL 0 | WARN 45 | SKIP 0 | PASS 572 ]
> 
> proc.time()
   user  system elapsed 
 960.68    6.21  974.10