##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:COTAN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings COTAN_2.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/COTAN.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘COTAN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COTAN’ version ‘2.6.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 for sufficient/correct file permissions ... 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘torch’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘ggplot2:::ggname’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
mergeUniformCellsClusters : fromMergedName: warning in
  vapply(currentClNames, function(clName, mergedName) {: partial
  argument match of 'FUN.VAL' to 'FUN.VALUE'
mergeUniformCellsClusters : fromMergedName: warning in
  return(str_detect(mergedName, clName)): partial argument match of
  'FUN.VAL' to 'FUN.VALUE'
mergeUniformCellsClusters : fromMergedName: warning in }, FUN.VAL =
  logical(1L), mergedClName): partial argument match of 'FUN.VAL' to
  'FUN.VALUE'
ECDPlot: no visible binding for global variable ‘.’
GDIPlot: no visible binding for global variable ‘sum.raw.norm’
GDIPlot: no visible binding for global variable ‘GDI’
UMAPPlot: no visible binding for global variable ‘x’
UMAPPlot: no visible binding for global variable ‘y’
UMAPPlot: no visible binding for global variable ‘types’
calculateCoex_Legacy: no visible binding for global variable
  ‘expectedNN’
calculateCoex_Legacy: no visible binding for global variable
  ‘expectedNY’
calculateCoex_Legacy: no visible binding for global variable
  ‘expectedYN’
calculateCoex_Legacy: no visible binding for global variable
  ‘expectedYY’
calculateCoex_Legacy: no visible binding for global variable
  ‘observedYY’
calculateCoex_Legacy: no visible binding for global variable ‘.’
calculateG: no visible binding for global variable ‘observedNN’
calculateG: no visible binding for global variable ‘observedNY’
calculateG: no visible binding for global variable ‘observedYN’
calculateG: no visible binding for global variable ‘observedYY’
calculateG: no visible binding for global variable ‘expectedNN’
calculateG: no visible binding for global variable ‘expectedNY’
calculateG: no visible binding for global variable ‘expectedYN’
calculateG: no visible binding for global variable ‘expectedYY’
calculatePartialCoex: no visible binding for global variable
  ‘expectedNN’
calculatePartialCoex: no visible binding for global variable
  ‘expectedNY’
calculatePartialCoex: no visible binding for global variable
  ‘expectedYN’
calculatePartialCoex: no visible binding for global variable
  ‘expectedYY’
calculatePartialCoex: no visible binding for global variable
  ‘observedYY’
calculatePartialCoex: no visible binding for global variable ‘.’
cellSizePlot: no visible binding for global variable ‘.’
cellsUniformClustering: no visible binding for global variable
  ‘objSeurat’
cellsUniformClustering: no visible binding for global variable
  ‘usedMaxResolution’
cellsUniformClustering: no visible binding for global variable
  ‘permMap’
checkClusterUniformity: no visible binding for global variable
  ‘pcaCellsPlot’
checkClusterUniformity: no visible binding for global variable ‘.’
checkClusterUniformity: no visible binding for global variable
  ‘bGroupGenesPlot’
checkClusterUniformity: no visible binding for global variable
  ‘UDEPLot’
checkClusterUniformity: no visible binding for global variable ‘nuPlot’
checkClusterUniformity: no visible binding for global variable
  ‘zoomedNuPlot’
cleanPlots: no visible binding for global variable ‘PC1’
cleanPlots: no visible binding for global variable ‘PC2’
cleanPlots: no visible binding for global variable ‘n’
cleanPlots: no visible binding for global variable ‘means’
cleanPlots: no visible binding for global variable ‘nu’
clustersMarkersHeatmapPlot: no visible binding for global variable
  ‘condName’
clustersMarkersHeatmapPlot: no visible binding for global variable
  ‘conditions’
clustersSummaryPlot: no visible binding for global variable ‘keys’
clustersSummaryPlot: no visible binding for global variable ‘values’
clustersSummaryPlot: no visible binding for global variable
  ‘CellNumber’
clustersSummaryPlot: no visible binding for global variable ‘ExpGenes’
clustersSummaryPlot: no visible binding for global variable ‘Cluster’
clustersSummaryPlot: no visible binding for global variable ‘Condition’
establishGenesClusters: no visible binding for global variable
  ‘secondaryMarkers’
establishGenesClusters: no visible binding for global variable ‘GCS’
establishGenesClusters: no visible binding for global variable
  ‘rankGenes’
expectedContingencyTables: no visible binding for global variable
  ‘expectedN’
expectedPartialContingencyTables: no visible binding for global
  variable ‘expectedNN’
expectedPartialContingencyTables: no visible binding for global
  variable ‘expectedN’
genesSizePlot: no visible binding for global variable ‘.’
geom_flat_violin : <anonymous>: no visible binding for global variable
  ‘group’
geom_flat_violin : <anonymous>: no visible binding for global variable
  ‘y’
geom_flat_violin : <anonymous>: no visible binding for global variable
  ‘x’
geom_flat_violin : <anonymous>: no visible binding for global variable
  ‘width’
geom_flat_violin : <anonymous>: no visible binding for global variable
  ‘violinwidth’
geom_flat_violin : <anonymous>: no visible binding for global variable
  ‘xmax’
geom_flat_violin : <anonymous>: no visible binding for global variable
  ‘xminv’
geom_flat_violin : <anonymous>: no visible binding for global variable
  ‘xmaxv’
heatmapPlot: no visible binding for global variable ‘obj’
heatmapPlot: no visible binding for global variable ‘type’
heatmapPlot: no visible binding for global variable ‘g2’
heatmapPlot: no visible binding for global variable ‘coex’
mergeUniformCellsClusters : fromMergedName: no visible binding for
  global variable ‘clName1’
mergeUniformCellsClusters : fromMergedName: no visible binding for
  global variable ‘clName2’
mergeUniformCellsClusters : testPairListMerge: no visible binding for
  global variable ‘cl1’
mergeUniformCellsClusters : testPairListMerge: no visible binding for
  global variable ‘cl2’
mergeUniformCellsClusters : mergeAllClusters : <anonymous>: no visible
  binding for global variable ‘clName1’
mergeUniformCellsClusters : mergeAllClusters : <anonymous>: no visible
  binding for global variable ‘clName2’
mergeUniformCellsClusters : mergeAllClusters: no visible binding for
  global variable ‘clName1’
mergeUniformCellsClusters : mergeAllClusters: no visible binding for
  global variable ‘clName2’
mergeUniformCellsClusters: no visible binding for global variable
  ‘permMap’
mitochondrialPercentagePlot: no visible binding for global variable ‘.’
mitochondrialPercentagePlot: no visible binding for global variable
  ‘mit.percentage’
observedContingencyTables: no visible binding for global variable
  ‘observedY’
observedPartialContingencyTables: no visible binding for global
  variable ‘observedYY’
observedPartialContingencyTables: no visible binding for global
  variable ‘observedY’
scatterPlot: no visible binding for global variable ‘.’
scatterPlot: no visible binding for global variable ‘.x’
calculateCoex,COTAN: no visible binding for global variable ‘useTorch’
coerce,COTAN-scCOTAN: no visible binding for global variable ‘rawNorm’
coerce,COTAN-scCOTAN: no visible binding for global variable ‘nu’
coerce,COTAN-scCOTAN: no visible binding for global variable ‘lambda’
coerce,COTAN-scCOTAN: no visible binding for global variable ‘a’
coerce,COTAN-scCOTAN: no visible binding for global variable ‘hk’
coerce,COTAN-scCOTAN: no visible binding for global variable ‘clusters’
coerce,COTAN-scCOTAN: no visible binding for global variable
  ‘clusterData’
Undefined global functions or variables:
  . .x CellNumber Cluster Condition ExpGenes GCS GDI PC1 PC2 UDEPLot a
  bGroupGenesPlot cl1 cl2 clName1 clName2 clusterData clusters coex
  condName conditions expectedN expectedNN expectedNY expectedYN
  expectedYY g2 group hk keys lambda means mit.percentage n nu nuPlot
  obj objSeurat observedNN observedNY observedY observedYN observedYY
  pcaCellsPlot permMap rankGenes rawNorm secondaryMarkers sum.raw.norm
  type types useTorch usedMaxResolution values violinwidth width x xmax
  xmaxv xminv y zoomedNuPlot
* 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         292.474  2.194 295.033
CalculatingCOEX          76.480  1.283  77.885
HeatmapPlots             52.186  1.217  53.627
HandlingClusterizations  35.739  0.854  36.659
ParametersEstimations    34.996  1.122  36.363
GenesStatistics          15.630  0.187  15.818
COTAN_ObjectCreation     13.623  0.234  13.861
Conversions               7.358  0.123   7.483
RawDataCleaning           6.030  0.146   6.187
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/COTAN.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL COTAN
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘COTAN’ ...
** 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 
  0.241   0.062   0.291 

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 
  0.221   0.066   0.273 

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 from [1:10] to [1:10]
Estimate dispersion: DONE
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: 2.9788339138031
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00130987167358398
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00678801536560059
Estimating genes' coex
Calculate genes' coex elapsed time: 1.01908302307129
Total calculations elapsed time: 4.00601482391357
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 4 genes batches from [1:2] to [7:8]
Executing 1 genes batches from [9:10] to [9:10]
Estimate dispersion: DONE
dispersion | min: 0.9033203125 | max: 4.6796875 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 4 cells batches from [1:3] to [10:11]
Executing 3 cells batches from [12:14] to [18:20]
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 from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 1.0362548828125 | max: 4.60986328125 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
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 from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.058837890625 | max: 3.528076171875 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
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 from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.32879638671875 | max: 4.0302734375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
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 from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.2294921875 | max: 3.8720703125 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
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 from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.2637939453125 | max: 3.929443359375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
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 from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.25177001953125 | max: 3.90966796875 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
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 from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.25592041015625 | max: 3.91650390625 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
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 from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.2545166015625 | max: 3.914306640625 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
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 from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.2550048828125 | max: 3.9150390625 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
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 from [1:10] to [1:10]
Estimate dispersion: DONE
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: 3.46092915534973
Calculating genes' coex normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.000844955444335938
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00400304794311523
Estimating genes' coex
Calculate genes' coex elapsed time: 1.09037685394287
Total calculations elapsed time: 4.55615401268005
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: 3.47711205482483
Calculating cells' coex normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.000873088836669922
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00283408164978027
Estimating cells' coex
Calculate cells' coex elapsed time: 1.20019388198853
Total calculations elapsed time: 4.6810131072998
Calculate cells' coex (legacy): 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 from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.903564453125 | max: 4.679443359375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
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 from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.0655517578125 | max: 3.5439453125 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
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: 0.61937543089282
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.3260498046875 | max: 4.026123046875 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
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 from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.23040771484375 | max: 3.8736572265625 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
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 from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.26348876953125 | max: 3.928955078125 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
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 0.026270214227825 | mean: 0.0240886952086962
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.2518310546875 | max: 3.9097900390625 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
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 from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.2559814453125 | max: 3.9166259765625 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
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 from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.25445556640625 | max: 3.9140625 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
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 from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.2550048828125 | max: 3.9150390625 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
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: 3.35895204544067
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.000638008117675781
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00164103507995605
Estimating genes' coex
Calculate genes' coex elapsed time: 1.19118881225586
Total calculations elapsed time: 4.55241990089417
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: 3.52487802505493
Calculating cells' coex normalization factor
Calculate cells' normalization factor elapsed time: 0.000658988952636719
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00165700912475586
Estimating cells' coex
Calculate cells' coex elapsed time: 1.20716595649719
Total calculations elapsed time: 4.73435997962952
Calculate cells' coex (legacy): DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
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 from [1:3] to [8:10]
Estimate dispersion: DONE
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: 3.33757996559143
Calculating genes' coex normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.000791072845458984
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00157594680786133
Estimating genes' coex
Calculate genes' coex elapsed time: 1.08962488174438
Total calculations elapsed time: 4.42957186698914
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: 3.47395515441895
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00066685676574707
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00176715850830078
Estimating genes' coex
Calculate genes' coex elapsed time: 1.08601188659668
Total calculations elapsed time: 4.56240105628967
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 from [1:3] to [8:10]
Estimate dispersion: DONE
dispersion | min: 0.903564453125 | max: 4.679443359375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 4 cells batches from [1:4] to [13:16]
Executing 1 cells batches from [17:20] to [17:20]
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 from [1:3] to [8:10]
Estimate dispersion: DONE
dispersion | min: 1.037109375 | max: 4.6107177734375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 4 cells batches from [1:4] to [13:16]
Executing 1 cells batches from [17:20] to [17:20]
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 from [1:3] to [8:10]
Estimate dispersion: DONE
dispersion | min: 1.03887939453125 | max: 4.6097412109375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 4 cells batches from [1:4] to [13:16]
Executing 1 cells batches from [17:20] to [17:20]
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: 3.3004879951477
Calculating cells' coex normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.000826835632324219
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00159621238708496
Estimating cells' coex
Calculate cells' coex elapsed time: 1.12613201141357
Total calculations elapsed time: 4.42904305458069
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 from [1:3] to [8:10]
Estimate dispersion: DONE
dispersion | min: 0.903564453125 | max: 4.679443359375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 4 cells batches from [1:4] to [13:16]
Executing 1 cells batches from [17:20] to [17:20]
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 from [1:3] to [8:10]
Estimate dispersion: DONE
dispersion | min: 1.037109375 | max: 4.6107177734375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 4 cells batches from [1:4] to [13:16]
Executing 1 cells batches from [17:20] to [17:20]
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 from [1:3] to [8:10]
Estimate dispersion: DONE
dispersion | min: 1.03887939453125 | max: 4.6097412109375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 4 cells batches from [1:4] to [13:16]
Executing 1 cells batches from [17:20] to [17:20]
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: 3.26668500900269
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.000628948211669922
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00147104263305664
Estimating genes' coex
Calculate genes' coex elapsed time: 1.14313387870789
Total calculations elapsed time: 4.4119188785553
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
S matrix sorted
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
S matrix sorted
Calculate GDI dataframe: DONE
Calculating S: START
Calculating S: DONE
S matrix sorted
S matrix sorted
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 from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 4.11122989654541
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: 5.06908702850342
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0097959041595459
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.071091890335083
Estimating genes' coex
Calculate genes' coex elapsed time: 1.11028909683228
Total calculations elapsed time: 6.26026391983032
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 7.36279797554016
Total elapsed time: 13.7509808540344
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 from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 4.13109397888184
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: 4.95195603370667
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0099489688873291
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0697929859161377
Estimating genes' coex
Calculate genes' coex elapsed time: 1.11846303939819
Total calculations elapsed time: 6.15016102790833
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 7.30870509147644
Total elapsed time: 13.7156889438629
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
S matrix sorted
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 from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 4.23769807815552
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: 5.16858196258545
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0137021541595459
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0791068077087402
Estimating genes' coex
Calculate genes' coex elapsed time: 1.12043118476868
Total calculations elapsed time: 6.38182210922241
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 7.60924196243286
Total elapsed time: 14.0931959152222
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
S matrix sorted
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 from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 4.21934604644775
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: 5.15638780593872
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0137851238250732
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0670778751373291
Estimating genes' coex
Calculate genes' coex elapsed time: 1.09492707252502
Total calculations elapsed time: 6.33217787742615
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 7.42387700080872
Total elapsed time: 13.8670239448547
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
S matrix sorted
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 from [1:569] to [1:569]
Estimate dispersion: DONE
dispersion | min: -0.2119140625 | max: 85.5 | % negative: 62.2144112478032
Cotan genes' coex estimation not requested
Total elapsed time: 6.72273397445679
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: 3.43415904045105
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00889110565185547
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00921201705932617
Estimating genes' coex
Calculate genes' coex elapsed time: 1.16979384422302
Total calculations elapsed time: 4.62205600738525
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: 3.5138509273529
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0081942081451416
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.016826868057251
Estimating genes' coex
Calculate genes' coex elapsed time: 1.16678094863892
Total calculations elapsed time: 4.70565295219421
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: 3.46369314193726
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00700902938842773
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00819897651672363
Estimating genes' coex
Calculate genes' coex elapsed time: 1.10221982002258
Total calculations elapsed time: 4.58112096786499
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
PCA: DONE
Hierarchical clustering: START
Hierarchical clustering: DONE
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Cotan genes' coex estimation not requested
Total elapsed time: 10.8830299377441
Saving elaborated data locally at: /tmp/Rtmp8kU3Sn/test.cotan.RDS
Creating cells' uniform clustering: START
In iteration 1 the number of cells to re-cluster is 1200 cells belonging to 0 clusters
Creating Seurat object: 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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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-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 
Negative:  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 
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-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 
Negative:  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 
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: 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
16:10:22 UMAP embedding parameters a = 0.9922 b = 1.112
16:10:22 Read 1200 rows and found 50 numeric columns
16:10:22 Using Annoy for neighbor search, n_neighbors = 30
16:10:22 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
16:10:22 Writing NN index file to temp file /tmp/Rtmp8kU3Sn/file3f3511f0e859
16:10:22 Searching Annoy index using 1 thread, search_k = 3000
16:10:22 Annoy recall = 100%
16:10:23 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
16:10:26 Initializing from normalized Laplacian + noise (using RSpectra)
16:10:26 Commencing optimization for 500 epochs, with 42274 positive edges
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
16:10:30 Optimization finished
Creating PDF UMAP in file:  /tmp/Rtmp8kU3Sn/test/reclustering/pdf_umap_1.pdf
Creating Seurat object: 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 from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.038818359375 | max: 11.109375 | % negative: 5
Only analysis elapsed time: 3.78262901306152
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: 3.80602312088013
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00838685035705566
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.053926944732666
Estimating genes' coex
Calculate genes' coex elapsed time: 1.21109509468079
Total calculations elapsed time: 5.07943201065063
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.29161500930786
Total elapsed time: 12.3461151123047
Checking uniformity for the cluster '01_0000' with 353 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
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
check.isCheckAbove = 0, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0.00833333333333333, check.thresholdRank = 0, check.quantileAtRatio = 1.44390094359268, check.quantileAtRank = NaN, isUniform = 1, 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 from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.0501708984375 | max: 14.515625 | % negative: 8.5
Only analysis elapsed time: 3.74610996246338
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: 3.80689001083374
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00832796096801758
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0486280918121338
Estimating genes' coex
Calculate genes' coex elapsed time: 1.14446187019348
Total calculations elapsed time: 5.00830793380737
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.16141605377197
Total elapsed time: 12.2755510807037
Checking uniformity for the cluster '01_0001' with 321 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
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
check.isCheckAbove = 0, 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 = 1, 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 from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.054443359375 | max: 104 | % negative: 36.5
Only analysis elapsed time: 3.6491641998291
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: 3.71990990638733
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0121221542358398
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0252058506011963
Estimating genes' coex
Calculate genes' coex elapsed time: 1.20610094070435
Total calculations elapsed time: 4.96333885192871
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.14428400993347
Total elapsed time: 12.1749920845032
Checking uniformity for the cluster '01_0002' with 295 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
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
check.isCheckAbove = 0, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0, check.thresholdRank = 0, check.quantileAtRatio = 1.39247518634893, check.quantileAtRank = NaN, isUniform = 1, 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 from [1:599] to [1:599]
Estimate dispersion: DONE
dispersion | min: -0.0662841796875 | max: 82.5 | % negative: 33.889816360601
Only analysis elapsed time: 3.71742701530457
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: 3.79518795013428
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00787997245788574
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0233240127563477
Estimating genes' coex
Calculate genes' coex elapsed time: 1.21691513061523
Total calculations elapsed time: 5.04330706596375
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.26492786407471
Total elapsed time: 12.398185968399
Checking uniformity for the cluster '01_0003' with 231 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
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
check.isCheckAbove = 0, 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 = 1, clusterSize = 231
cluster 01_0003 is uniform


Found 4 uniform and  0 non-uniform clusters
NO new possible uniform clusters! 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 from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.054443359375 | max: 104 | % negative: 36.5
Only analysis elapsed time: 3.82599782943726
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: 3.91552305221558
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0101399421691895
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0240850448608398
Estimating genes' coex
Calculate genes' coex elapsed time: 1.18864703178406
Total calculations elapsed time: 5.13839507102966
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.22585105895996
Total elapsed time: 12.3843839168549
Checking uniformity for the cluster 'Cluster_2' with 295 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
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
firstCheck.isCheckAbove = 0, 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 = 1, 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 = 0, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = NaN, thirdCheck.maxRankBeyond = 2, thirdCheck.fractionBeyond = NaN, thirdCheck.thresholdRank = 5, thirdCheck.quantileAtRatio = NaN, thirdCheck.quantileAtRank = 1.4279762218014, isUniform = 1, 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
Creating Seurat object: 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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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-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 
Negative:  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 
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-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 
Negative:  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 
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: 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
16:12:19 UMAP embedding parameters a = 0.9922 b = 1.112
16:12:19 Read 1200 rows and found 50 numeric columns
16:12:19 Using Annoy for neighbor search, n_neighbors = 30
16:12:19 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
16:12:20 Writing NN index file to temp file /tmp/Rtmp8kU3Sn/file3f354f466865
16:12:20 Searching Annoy index using 1 thread, search_k = 3000
16:12:20 Annoy recall = 100%
16:12:21 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
16:12:24 Initializing from normalized Laplacian + noise (using RSpectra)
16:12:24 Commencing optimization for 500 epochs, with 42274 positive edges
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
16:12:28 Optimization finished
Creating PDF UMAP in file:  /tmp/Rtmp8kU3Sn/test/reclustering/pdf_umap_1.pdf
Creating Seurat object: DONE
Using passed in clusterization
* 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 from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.0386962890625 | max: 19.40625 | % negative: 6.5
Only analysis elapsed time: 3.86508893966675
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: 4.38260793685913
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00841116905212402
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0706789493560791
Estimating genes' coex
Calculate genes' coex elapsed time: 1.19270300865173
Total calculations elapsed time: 5.65440106391907
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.89623403549194
Total elapsed time: 13.1165990829468
Checking uniformity for the cluster '01_0001' with 600 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
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
firstCheck.isCheckAbove = 0, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0383333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.38474391612669, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = 1, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.035, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42418110276823, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = 0, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = NaN, thirdCheck.maxRankBeyond = 2, thirdCheck.fractionBeyond = NaN, thirdCheck.thresholdRank = 4, thirdCheck.quantileAtRatio = NaN, thirdCheck.quantileAtRank = 1.51521594648005, isUniform = 1, 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 from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.032958984375 | max: 10.0859375 | % negative: 3.66666666666667
Only analysis elapsed time: 3.78954696655273
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: 4.19547390937805
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0081179141998291
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0570321083068848
Estimating genes' coex
Calculate genes' coex elapsed time: 1.16648101806641
Total calculations elapsed time: 5.42710494995117
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.63936805725098
Total elapsed time: 12.7312529087067
Checking uniformity for the cluster '01_0002' with 600 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
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
firstCheck.isCheckAbove = 0, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0366666666666667, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.37665544944666, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = 1, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.0316666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42305229982217, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = 0, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = NaN, thirdCheck.maxRankBeyond = 2, thirdCheck.fractionBeyond = NaN, thirdCheck.thresholdRank = 2, thirdCheck.quantileAtRatio = NaN, thirdCheck.quantileAtRank = 1.50182972335853, isUniform = 1, clusterSize = 600
cluster 01_0002 is uniform


Found 2 uniform and  0 non-uniform clusters
NO new possible uniform clusters! 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 from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.0501708984375 | max: 14.515625 | % negative: 8.5
Only analysis elapsed time: 3.7048180103302
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: 3.93616604804993
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00830984115600586
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0493049621582031
Estimating genes' coex
Calculate genes' coex elapsed time: 1.17639803886414
Total calculations elapsed time: 5.17017889022827
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.35754299163818
Total elapsed time: 12.4102330207825
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
[1] "Tested cluster: 3"
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 from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.038818359375 | max: 11.109375 | % negative: 5
Only analysis elapsed time: 3.72391390800476
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: 4.05277299880981
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00906801223754883
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0539939403533936
Estimating genes' coex
Calculate genes' coex elapsed time: 1.20290803909302
Total calculations elapsed time: 5.31874299049377
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.5862500667572
Total elapsed time: 12.6757919788361
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
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 from [1:600] to [1:600]
Estimate dispersion: DONE
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 from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Cotan genes' coex estimation not requested
Total elapsed time: 7.83180499076843
Creating Seurat object: 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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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-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 
Negative:  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 
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-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 
Negative:  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 
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: 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
16:14:21 UMAP embedding parameters a = 0.9922 b = 1.112
16:14:21 Read 1200 rows and found 50 numeric columns
16:14:21 Using Annoy for neighbor search, n_neighbors = 30
16:14:21 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
16:14:21 Writing NN index file to temp file /tmp/Rtmp8kU3Sn/file3f3526a02fc7
16:14:21 Searching Annoy index using 1 thread, search_k = 3000
16:14:22 Annoy recall = 100%
16:14:23 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
16:14:25 Initializing from normalized Laplacian + noise (using RSpectra)
16:14:25 Commencing optimization for 500 epochs, with 42274 positive edges
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
16:14:29 Optimization finished
Creating Seurat object: DONE
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 from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Cotan genes' coex estimation not requested
Total elapsed time: 8.02757096290588
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 from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 4.36671304702759
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: 5.12136006355286
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00829505920410156
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0668950080871582
Estimating genes' coex
Calculate genes' coex elapsed time: 1.24284791946411
Total calculations elapsed time: 6.43939805030823
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 7.64974093437195
Total elapsed time: 14.5114569664001
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
S matrix sorted
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
S matrix sorted
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
S matrix sorted
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 from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Cotan genes' coex estimation not requested
Total elapsed time: 7.83195495605469
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 1.43530796540673
Handling cluster '2' with mean UDE 0.640931107489518
Handling cluster '3' with mean UDE 0.546546914955574
Handling cluster '4' with mean UDE 1.22034802329656
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 from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.0340576171875 | max: 10.4375 | % negative: 4.33333333333333
Only analysis elapsed time: 3.969407081604
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: 4.49094009399414
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0100650787353516
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0612368583679199
Estimating genes' coex
Calculate genes' coex elapsed time: 1.2438600063324
Total calculations elapsed time: 5.80610203742981
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.99992108345032
Total elapsed time: 13.4531991481781
Checking uniformity for the cluster '1_2-merge' with 574 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
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
firstCheck.isCheckAbove = 0, 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 = 1, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.28, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.41724738266284, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = 0, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = NaN, thirdCheck.maxRankBeyond = 2, thirdCheck.fractionBeyond = NaN, thirdCheck.thresholdRank = 20, thirdCheck.quantileAtRatio = NaN, thirdCheck.quantileAtRank = 1.5067755752749, isUniform = 0, 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 from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.03839111328125 | max: 17.40625 | % negative: 6.66666666666667
Only analysis elapsed time: 3.96216797828674
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: 4.46292901039124
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00951886177062988
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0546040534973145
Estimating genes' coex
Calculate genes' coex elapsed time: 1.16078495979309
Total calculations elapsed time: 5.68783688545227
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.91338300704956
Total elapsed time: 13.3297159671783
Checking uniformity for the cluster '3_4-merge' with 626 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
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
firstCheck.isCheckAbove = 0, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.248333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.38846117443453, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = 1, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.218333333333333, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42066795244754, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = 0, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = NaN, thirdCheck.maxRankBeyond = 2, thirdCheck.fractionBeyond = NaN, thirdCheck.thresholdRank = 22, thirdCheck.quantileAtRatio = NaN, thirdCheck.quantileAtRank = 1.52592182249634, isUniform = 0, 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 from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.0390625 | max: 12.59375 | % negative: 9.16666666666667
Only analysis elapsed time: 3.78570795059204
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: 4.06819105148315
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00931501388549805
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.040841817855835
Estimating genes' coex
Calculate genes' coex elapsed time: 1.09857702255249
Total calculations elapsed time: 5.21692490577698
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.34478092193604
Total elapsed time: 12.4955139160156
Checking uniformity for the cluster '2_3-merge' with 536 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
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
firstCheck.isCheckAbove = 0, 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 = 1, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.251666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.45276697088287, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = 0, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = NaN, thirdCheck.maxRankBeyond = 2, thirdCheck.fractionBeyond = NaN, thirdCheck.thresholdRank = 30, thirdCheck.quantileAtRatio = NaN, thirdCheck.quantileAtRank = 1.54477108741148, isUniform = 0, 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 from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.04754638671875 | max: 10.234375 | % negative: 5
Only analysis elapsed time: 3.87760519981384
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: 4.22019410133362
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00860500335693359
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0550010204315186
Estimating genes' coex
Calculate genes' coex elapsed time: 1.27485585212708
Total calculations elapsed time: 5.55865597724915
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.74436187744141
Total elapsed time: 12.9407210350037
Checking uniformity for the cluster '2_4-merge' with 532 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
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
firstCheck.isCheckAbove = 0, 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 = 1, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.361666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.5559961079834, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = 0, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = NaN, thirdCheck.maxRankBeyond = 2, thirdCheck.fractionBeyond = NaN, thirdCheck.thresholdRank = 109, thirdCheck.quantileAtRatio = NaN, thirdCheck.quantileAtRank = 1.68475283375667, isUniform = 0, 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 from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.046630859375 | max: 9.03515625 | % negative: 1.33333333333333
Only analysis elapsed time: 4.03301906585693
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: 4.41945385932922
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0083000659942627
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0578200817108154
Estimating genes' coex
Calculate genes' coex elapsed time: 1.15815186500549
Total calculations elapsed time: 5.6437258720398
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.80058598518372
Total elapsed time: 13.2135369777679
Checking uniformity for the cluster '1_3-merge' with 668 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
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
firstCheck.isCheckAbove = 0, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.33, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.57492370740536, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = 1, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.31, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.63687557073409, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = 0, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = NaN, thirdCheck.maxRankBeyond = 2, thirdCheck.fractionBeyond = NaN, thirdCheck.thresholdRank = 77, thirdCheck.quantileAtRatio = NaN, thirdCheck.quantileAtRank = 1.68881338289982, isUniform = 0, 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 from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.0164794921875 | max: 5.5595703125 | % negative: 0.166666666666667
Only analysis elapsed time: 3.79132699966431
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: 4.31366586685181
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00998210906982422
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0644590854644775
Estimating genes' coex
Calculate genes' coex elapsed time: 1.1496319770813
Total calculations elapsed time: 5.53773903846741
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.71964287757874
Total elapsed time: 12.8450191020966
Checking uniformity for the cluster '1_4-merge' with 664 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
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
firstCheck.isCheckAbove = 0, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.348333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.53527735568611, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = 1, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.316666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.55951216335004, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = 0, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = NaN, thirdCheck.maxRankBeyond = 2, thirdCheck.fractionBeyond = NaN, thirdCheck.thresholdRank = 59, thirdCheck.quantileAtRatio = NaN, thirdCheck.quantileAtRank = 1.64605433203112, isUniform = 0, 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 from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 4.35083889961243
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: 5.27277612686157
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00801491737365723
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0676920413970947
Estimating genes' coex
Calculate genes' coex elapsed time: 1.18945407867432
Total calculations elapsed time: 6.53793716430664
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 7.72662401199341
Total elapsed time: 14.541079044342
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
S matrix sorted
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
firstCheck.isCheckAbove = 0, 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 = 1, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.388333333333333, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.61240081401511, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = 0, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = NaN, thirdCheck.maxRankBeyond = 2, thirdCheck.fractionBeyond = NaN, thirdCheck.thresholdRank = 90, thirdCheck.quantileAtRatio = NaN, thirdCheck.quantileAtRank = 1.66512085964762, isUniform = 0, 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 from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.0340576171875 | max: 10.4375 | % negative: 4.33333333333333
Only analysis elapsed time: 3.87647795677185
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: 4.19747591018677
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00933098793029785
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0577869415283203
Estimating genes' coex
Calculate genes' coex elapsed time: 1.17880702018738
Total calculations elapsed time: 5.44340085983276
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.63736796379089
Total elapsed time: 12.8825190067291
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
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 from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.03839111328125 | max: 17.40625 | % negative: 6.66666666666667
Only analysis elapsed time: 3.93307685852051
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: 4.33246898651123
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0111401081085205
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.057837963104248
Estimating genes' coex
Calculate genes' coex elapsed time: 1.15434789657593
Total calculations elapsed time: 5.55579495429993
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.72967505455017
Total elapsed time: 13.1025369167328
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 489 ]
> 
> proc.time()
   user  system elapsed 
944.493   7.063 952.249