Multiple platform build/check report for BioC 3.21 - CHECK results for COTAN on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4833
merida1	macOS 12.7.6 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4614
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4555
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4586
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for COTAN on kunpeng2

To the developers/maintainers of the COTAN package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/COTAN.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: COTAN

Version: 2.8.5

Command: /home/biocbuild/R/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings COTAN_2.8.5.tar.gz

StartedAt: 2025-10-14 07:52:53 -0000 (Tue, 14 Oct 2025)

EndedAt: 2025-10-14 08:24:04 -0000 (Tue, 14 Oct 2025)

EllapsedTime: 1871.1 seconds

RetCode: 0

Status: WARNINGS

CheckDir: COTAN.Rcheck

Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings COTAN_2.8.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/COTAN.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘COTAN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COTAN’ version ‘2.8.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... WARNING
'library' or 'require' call to ‘torch’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing or unexported object: ‘zeallot::zeallous’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ECDPlot: no visible binding for global variable ‘.’
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 ‘pca’
cellsUniformClustering: no visible binding for global variable
  ‘resolution’
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’
clustersMarkersHeatmapPlot: no visible binding for global variable
  ‘condName’
clustersMarkersHeatmapPlot: no visible binding for global variable
  ‘conditions’
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 ‘.’
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 ‘.’
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 ‘.’
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:
  . GCS UDEPLot a bGroupGenesPlot cl1 cl2 clName1 clName2 clusterData
  clusters condName conditions expectedN expectedNN expectedNY
  expectedYN expectedYY hk lambda nu nuPlot observedNN observedNY
  observedY observedYN observedYY pca pcaCellsPlot permMap rankGenes
  rawNorm resolution secondaryMarkers useTorch usedMaxResolution
  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         250.703  0.709 249.103
CalculatingCOEX          73.777  0.236  71.592
HandlingClusterizations  58.176  0.159  57.848
HeatmapPlots             47.845  0.283  46.482
ParametersEstimations    34.354  0.208  34.632
GenesStatistics          15.261  0.043  14.827
COTAN_ObjectCreation     13.787  1.475  14.744
Conversions               7.854  0.028   7.897
RawDataCleaning           7.181  0.015   7.219
* 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: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/COTAN.Rcheck/00check.log’
for details.

Installation output

COTAN.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL COTAN
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘COTAN’ ...
** this is package ‘COTAN’ version ‘2.8.5’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (COTAN)

Tests output

COTAN.Rcheck/tests/outputTestDatasetCreation.Rout


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 
  0.203   0.031   0.220

COTAN.Rcheck/tests/spelling.Rout


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 
  0.207   0.019   0.216

COTAN.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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

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

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

> Sys.setenv(R_TESTS = "")
> library(testthat)
> library(COTAN)
> test_check("COTAN")
Setting new log level to 4
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.9033203125 | max: 4.6796875 | % negative: 10
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.17217755317688
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00129294395446777
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00840401649475098
Estimating genes' coex
Calculate genes' coex elapsed time: 1.03426027297974
Total calculations elapsed time: 4.21613478660583
Calculate genes' coex (legacy): DONE
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 5 genes batches
`dispersion` | min: 0.9033203125 | max: 4.6796875 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 7 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75595238095238 | median:  1.07174634176587 | mean:  1.07174634176587
Estimate `dispersion`/`nu`: START
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 1.0362548828125 | max: 4.60986328125 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0265938895089288 | median:  0.0144680038331048 | mean:  0.0144680038331048
`nu` mean: 1.69633192486233
Marginal errors | max: 1.95570586131367 | median 1.32068160171502 | mean: 1.33375826507259
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.058837890625 | max: 3.528076171875 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.416683423613994 | median:  0.239880630367975 | mean:  0.239880630367975
`nu` mean: 0.823197206753982
Marginal errors | max: 0.836359531101206 | median 0.703684202571891 | mean: 0.645537958989614
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.32879638671875 | max: 4.0302734375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.164237872898673 | median:  0.0955985184389135 | mean:  0.0955985184389135
`nu` mean: 1.06863935445976
Marginal errors | max: 0.259872988828242 | median 0.213703042752633 | mean: 0.197386407582083
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2294921875 | max: 3.8720703125 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.055185575120883 | median:  0.0319991762044448 | mean:  0.0319991762044448
`nu` mean: 0.976813601083562
Marginal errors | max: 0.0951586919577032 | median 0.079429703709466 | mean: 0.0724140148396648
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2637939453125 | max: 3.929443359375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0196211148938294 | median:  0.01138609597457 | mean:  0.01138609597457
`nu` mean: 1.00823501891926
Marginal errors | max: 0.0327747321002292 | median 0.0272104747849538 | mean: 0.0248963830312038
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.25177001953125 | max: 3.90966796875 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00670099066960717 | median:  0.00388888266671264 | mean:  0.00388888266671264
`nu` mean: 0.997187891997105
Marginal errors | max: 0.0114324509186883 | median 0.0094232649770607 | mean: 0.00863113610779571
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.25592041015625 | max: 3.91650390625 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00230093811689414 | median:  0.00132529122122246 | mean:  0.00132529122122246
`nu` mean: 1.00097564689567
Marginal errors | max: 0.00387133150664631 | median 0.0031091017608853 | mean: 0.00286071175800213
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2545166015625 | max: 3.914306640625 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.000837011646904529 | median:  0.000470837393363011 | mean:  0.000470837393363011
`nu` mean: 0.999633825746458
Marginal errors | max: 0.00122501723202006 | median 0.00102126435760308 | mean: 0.000943992659051318
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2550048828125 | max: 3.9150390625 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.000209227351122054 | median:  0.000122070312500028 | mean:  0.000122070312500028
`nu` mean: 1.00008715703862
Marginal errors | max: 0.000364602956581805 | median 0.000313956936819793 | mean: 0.000282899574318485
Estimate `dispersion`/`nu`: DONE
Estimate `dispersion`/`nu`: START
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.9033203125 | max: 4.6796875 | % negative: 10
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet

Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.17831802368164
Calculating genes' coex normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.000952482223510742
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00408172607421875
Estimating genes' coex
Calculate genes' coex elapsed time: 1.06935286521912
Total calculations elapsed time: 4.25270509719849
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: 3.12515258789062
Calculating cells' coex normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.0009918212890625
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00307202339172363
Estimating cells' coex
Calculate cells' coex elapsed time: 1.03337383270264
Total calculations elapsed time: 4.16259026527405
Calculate cells' coex (legacy): DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Running genes' selection: START
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Running genes' selection: START
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Running genes' selection: START
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Selected 5 genes using HGDI selector
Running genes' selection: DONE
Running genes' selection: START
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Selected 5 genes using HVG_Seurat selector
Running genes' selection: DONE
Running genes' selection: START
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer data
Calculating gene means
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variance to mean ratios
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Running genes' selection: START
Given 5 genes as input
Running genes' selection: DONE
Initializing `COTAN` meta-data
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate `dispersion`/`nu`: START
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.903564453125 | max: 4.679443359375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75719246031746 | median:  1.07229953342014 | mean:  1.07229953342014
`nu` mean: 1.68489292689732
Marginal errors | max: 1.73564890252257 | median 1.37996360874076 | mean: 1.32180348113228
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.0655517578125 | max: 3.5439453125 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.402649984216273 | median:  0.231868788425666 | mean:  0.231868788425666
`nu` mean: 0.829218804209393
Marginal errors | max: 0.80321315986594 | median 0.677497553540581 | mean: 0.619375430892821
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.3260498046875 | max: 4.026123046875 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.158004893526231 | median:  0.0919692884670312 | mean:  0.0919692884670312
`nu` mean: 1.0660356050592
Marginal errors | max: 0.250724014302326 | median 0.206232152124436 | mean: 0.190425623677198
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.23040771484375 | max: 3.8736572265625 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0532774732102337 | median:  0.0308837890624999 | mean:  0.0308837890624999
`nu` mean: 0.977606315852266
Marginal errors | max: 0.0916983669060123 | median 0.0765266929824948 | mean: 0.0697593208689684
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.26348876953125 | max: 3.928955078125 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0189966206463044 | median:  0.0110199320575908 | mean:  0.0110199320575908
`nu` mean: 1.00797668858871
Marginal errors | max: 0.0317151207459254 | median 0.0262702142278251 | mean: 0.0240886952086962
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2518310546875 | max: 3.9097900390625 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00670088501353994 | median:  0.00388888101583662 | mean:  0.00388888101583662
`nu` mean: 0.997187996002297
Marginal errors | max: 0.0113693316356223 | median 0.00939669372836249 | mean: 0.00860715734056932
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2559814453125 | max: 3.9166259765625 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00251007446998996 | median:  0.00144735987374958 | mean:  0.00144735987374958
`nu` mean: 1.00106271459624
Marginal errors | max: 0.00406746973787442 | median 0.00343393462175534 | mean: 0.00313496757119527
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.25445556640625 | max: 3.9140625 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.000837027590858019 | median:  0.000488281249999889 | mean:  0.000488281249999889
`nu` mean: 0.999651253659142
Marginal errors | max: 0.00143433714371533 | median 0.00116636244706747 | mean: 0.00109289166947839
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2550048828125 | max: 3.9150390625 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.000209227688885871 | median:  0.0001220703125 | mean:  0.0001220703125
`nu` mean: 1.00008715737639
Marginal errors | max: 0.000379524846207957 | median 0.000325685250686547 | mean: 0.000295532844332236
Estimate `dispersion`/`nu`: DONE
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet

Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.07077240943909
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.000733137130737305
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00194954872131348
Estimating genes' coex
Calculate genes' coex elapsed time: 0.996618270874023
Total calculations elapsed time: 4.07007336616516
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: 3.06337118148804
Calculating cells' coex normalization factor
Calculate cells' normalization factor elapsed time: 0.00075984001159668
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00206303596496582
Estimating cells' coex
Calculate cells' coex elapsed time: 1.03416728973389
Total calculations elapsed time: 4.10036134719849
Calculate cells' coex (legacy): DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Calculate genes' partial coex: START
Retrieving expected genes' partial contingency table
calculating partial NN.. done
calculating partial NY..YN..YY.. done
Calculating genes' partial coex normalization factor
Fraction of genes with very low expected contingency tables: 0.325
Retrieving observed genes' yes/yes partial contingency table
calculating partial YY.. done
Estimating genes' partial coex
Calculate genes' partial coex: DONE
Calculate cells' partial coex: START
Retrieving expected cells' partial contingency table
calculating partial NN.. done
calculating partial YN..NY..YY.. done
Calculating cells' partial coex normalization factor
Fraction of genes with very low expected contingency tables: 0
Retrieving observed cells' yes/yes partial contingency table
calculating partial YY.. done
Estimating cells' partial coex
Calculate cells' partial coex: DONE
Asked to drop 2 genes and 0 cells
Asked to drop 0 genes and 4 cells
Asked to drop 2 genes and 2 cells

Attaching package: 'rlang'

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

    is_false, is_null, is_true

Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
calculating YY.. done
calculating YY.. done
calculating YN..NY..NN..t().. done
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
`dispersion` | min: 0.9033203125 | max: 4.6796875 | % negative: 10
calculating NN.. done
calculating NN.. done
calculating NY..YN..YY..t().. done
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.10581922531128
Calculating genes' coex normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.000968456268310547
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0020904541015625
Estimating genes' coex
Calculate genes' coex elapsed time: 1.02409172058105
Total calculations elapsed time: 4.13296985626221
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: 3.11519432067871
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.000710010528564453
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00202512741088867
Estimating genes' coex
Calculate genes' coex elapsed time: 1.042072057724
Total calculations elapsed time: 4.16000151634216
Calculate genes' coex (legacy): DONE
Calculate genes' partial coex: START
Retrieving expected genes' partial contingency table
calculating partial NN.. done
calculating partial NY..YN..YY.. done
Calculating genes' partial coex normalization factor
Fraction of genes with very low expected contingency tables: 0.1
Retrieving observed genes' yes/yes partial contingency table
calculating partial YY.. done
Estimating genes' partial coex
Calculate genes' partial coex: DONE
Calculate genes' partial coex: START
Retrieving expected genes' partial contingency table
calculating partial NN.. done
calculating partial NY..YN..YY.. done
Calculating genes' partial coex normalization factor
Fraction of genes with very low expected contingency tables: 0.4
Retrieving observed genes' yes/yes partial contingency table
calculating partial YY.. done
Estimating genes' partial coex
Calculate genes' partial coex: DONE
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
calculating YY.. done
calculating YY.. done
calculating NY..YN..NN..t().. done
Estimate `dispersion`/`nu`: START
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
`dispersion` | min: 0.903564453125 | max: 4.679443359375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75719246031746 | median:  1.07229953342014 | mean:  1.07229953342014
`nu` mean: 1.68489292689732
Marginal errors | max: 0.25535328937316 | median 0.0807577993228135 | mean: 0.101980750205762
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
`dispersion` | min: 1.037109375 | max: 4.6107177734375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0273438105507502 | median:  0.0148852611818011 | mean:  0.0148852611818011
`nu` mean: 1.69735147626627
Marginal errors | max: 0.00326864580272002 | median 0.00111524657842743 | mean: 0.00131556083122533
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
`dispersion` | min: 1.03887939453125 | max: 4.6097412109375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0 | median:  0 | mean:  0
`nu` mean: 1.69735147626627
Marginal errors | max: 7.56328383637594e-05 | median 1.72948087246994e-05 | mean: 2.99252342145451e-05
Estimate `dispersion`/`nu`: DONE
calculating NN.. done
calculating NN.. done
calculating YN..NY..YY..t().. done
Calculate cells' coex (legacy): START
Retrieving expected cells' contingency table
calculating NN.. done
calculating YN..NY..YY..t().. done
Expected cells' contingency table elapsed time: 3.09112906455994
Calculating cells' coex normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.000973939895629883
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00205564498901367
Estimating cells' coex
Calculate cells' coex elapsed time: 1.04734444618225
Total calculations elapsed time: 4.14150309562683
Calculate cells' coex (legacy): DONE
Calculate cells' partial coex: START
Retrieving expected cells' partial contingency table
calculating partial NN.. done
calculating partial YN..NY..YY.. done
Calculating cells' partial coex normalization factor
Fraction of genes with very low expected contingency tables: 0
Retrieving observed cells' yes/yes partial contingency table
calculating partial YY.. done
Estimating cells' partial coex
Calculate cells' partial coex: DONE
Calculate cells' partial coex: START
Retrieving expected cells' partial contingency table
calculating partial NN.. done
calculating partial YN..NY..YY.. done
Calculating cells' partial coex normalization factor
Fraction of genes with very low expected contingency tables: 0
Retrieving observed cells' yes/yes partial contingency table
calculating partial YY.. done
Estimating cells' partial coex
Calculate cells' partial coex: DONE
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate `dispersion`/`nu`: START
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
`dispersion` | min: 0.903564453125 | max: 4.679443359375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75719246031746 | median:  1.07229953342014 | mean:  1.07229953342014
`nu` mean: 1.68489292689732
Marginal errors | max: 0.25535328937316 | median 0.0807577993228135 | mean: 0.101980750205762
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
`dispersion` | min: 1.037109375 | max: 4.6107177734375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0273438105507502 | median:  0.0148852611818011 | mean:  0.0148852611818011
`nu` mean: 1.69735147626627
Marginal errors | max: 0.00326864580272002 | median 0.00111524657842743 | mean: 0.00131556083122533
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
`dispersion` | min: 1.03887939453125 | max: 4.6097412109375 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Estimate `nu`: DONE
`nu` change (abs) | max: 0 | median:  0 | mean:  0
`nu` mean: 1.69735147626627
Marginal errors | max: 7.56328383637594e-05 | median 1.72948087246994e-05 | mean: 2.99252342145451e-05
Estimate `dispersion`/`nu`: DONE
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.1058235168457
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.000739812850952148
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00212240219116211
Estimating genes' coex
Calculate genes' coex elapsed time: 1.11011505126953
Total calculations elapsed time: 4.21880078315735
Calculate genes' coex (legacy): DONE
Calculating S: START
Calculating S: DONE
Calculating G: START
calculating YY.. done
calculating YN..NY..NN..t().. done
calculating NN.. done
calculating NY..YN..YY..t().. done
Estimating G
Calculating G: DONE
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values genome wide on columns and genome wide on rows
calculating PValues: DONE
Using G
Calculating G: START
calculating YY.. done
calculating YN..NY..NN..t().. done
calculating NN.. done
calculating NY..YN..YY..t().. done
Estimating G
Calculating G: DONE
calculating PValues: START
Get p-values on a set of genes on columns and on a set of genes on rows
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Calculate GDI dataframe: START
Using G
Calculating G: START
calculating YY.. done
calculating YN..NY..NN..t().. done
calculating NN.. done
calculating NY..YN..YY..t().. done
Estimating G
Calculating G: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Initializing `COTAN` meta-data
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 4.25138115882874
Cotan genes' coex estimation started
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.85053038597107
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0193386077880859
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0521059036254883
Estimating genes' coex
Calculate genes' coex elapsed time: 1.03031778335571
Total calculations elapsed time: 4.95229268074036
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.02800869941711
Total elapsed time: 12.3924369812012
Initializing `COTAN` meta-data
Condition test
n cells 1200
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 4.3401792049408
Cotan genes' coex estimation started
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.85014128684998
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0190205574035645
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0513484477996826
Estimating genes' coex
Calculate genes' coex elapsed time: 1.03097200393677
Total calculations elapsed time: 4.95148229598999
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.00017070770264
Total elapsed time: 12.4208481311798
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Condition test
n cells 1200
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 4.30539560317993
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: 3.75266981124878
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0194528102874756
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0513536930084229
Estimating genes' coex
Calculate genes' coex elapsed time: 1.04932498931885
Total calculations elapsed time: 4.87280130386353
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.91275310516357
Total elapsed time: 12.3285026550293
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Condition test
n cells 1200
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 4.20076966285706
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: 3.70847868919373
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.018869161605835
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0512571334838867
Estimating genes' coex
Calculate genes' coex elapsed time: 1.02650666236877
Total calculations elapsed time: 4.80511164665222
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.83387160301208
Total elapsed time: 12.0971596240997
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Asked to drop 0 genes and 1160 cells
Cotan analysis functions started
Asked to drop 31 genes and 0 cells
Genes/cells selection done: dropped [31] genes and [0] cells
Working on [569] genes and [40] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.2119140625 | max: 85.5 | % negative: 62.2144112478032
Cotan genes' coex estimation not requested
Total elapsed time: 6.15597128868103
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: 3.11358952522278
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0169188976287842
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00789928436279297
Estimating genes' coex
Calculate genes' coex elapsed time: 1.01782560348511
Total calculations elapsed time: 4.15623331069946
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: 3.14268946647644
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0170145034790039
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00783348083496094
Estimating genes' coex
Calculate genes' coex elapsed time: 1.02872133255005
Total calculations elapsed time: 4.19625878334045
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: 3.17724871635437
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0177233219146729
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00792837142944336
Estimating genes' coex
Calculate genes' coex elapsed time: 1.02365446090698
Total calculations elapsed time: 4.22655487060547
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
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Cotan genes' coex estimation not requested
Total elapsed time: 11.5114073753357
Saving elaborated data locally at: /home/biocbuild/tmp/RtmpnFtjLL/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
Asked to drop no genes or cells
Running genes' selection: START
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Selected 600 genes using HVG_Seurat selector
Running genes' selection: DONE
Creating Seurat object: START
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
PC_ 1 
Positive:  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 
Negative:  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 
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-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 
Negative:  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 
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-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 
Negative:  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 
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1200
Number of edges: 55489

Running Louvain algorithm with multilevel refinement...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5973
Number of communities: 4
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 0.8
Creating Seurat object: DONE
Creating PDF UMAP in file:  /home/biocbuild/tmp/RtmpnFtjLL/test/reclustering/pdf_umap_1.pdf
UMAP plot
Calculating UMAP: START
08:15:53 UMAP embedding parameters a = 0.9922 b = 1.112
08:15:53 Read 1200 rows and found 40 numeric columns
08:15:53 Using Annoy for neighbor search, n_neighbors = 30
08:15:53 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
08:15:53 Writing NN index file to temp file /home/biocbuild/tmp/RtmpnFtjLL/file159fb628e720b
08:15:53 Searching Annoy index using 1 thread, search_k = 3000
08:15:53 Annoy recall = 100%
08:15:54 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
08:15:57 Initializing from normalized Laplacian + noise (using RSpectra)
08:15:57 Commencing optimization for 500 epochs, with 42618 positive edges
08:15:57 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
08:16:00 Optimization finished
Calculating UMAP: DONE
UMAP plot
Calculating UMAP: START
08:16:00 UMAP embedding parameters a = 0.9922 b = 1.112
08:16:00 Read 1200 rows and found 40 numeric columns
08:16:00 Using Annoy for neighbor search, n_neighbors = 30
08:16:00 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
08:16:00 Writing NN index file to temp file /home/biocbuild/tmp/RtmpnFtjLL/file159fb1664f46f
08:16:00 Searching Annoy index using 1 thread, search_k = 3000
08:16:01 Annoy recall = 100%
08:16:02 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
08:16:04 Initializing from normalized Laplacian + noise (using RSpectra)
08:16:04 Commencing optimization for 500 epochs, with 42618 positive edges
08:16:04 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
08:16:07 Optimization finished
Calculating UMAP: DONE
* checking uniformity of cluster '0' of 4 clusters
Asked to drop 0 genes and 847 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [353] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.038818359375 | max: 11.109375 | % negative: 5
Only analysis elapsed time: 3.61270451545715
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: 3.57678961753845
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0216236114501953
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0411050319671631
Estimating genes' coex
Calculate genes' coex elapsed time: 1.12655448913574
Total calculations elapsed time: 4.76607275009155
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.90895676612854
Total elapsed time: 11.7603394985199
Checking uniformity for the cluster '01_0000' with 353 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0000, with size 353, is uniform
Cluster 01_0000's shift to uniformity: -0.01609905640731
class = SimpleGDIUniformityCheck, check.isCheckAbove = FALSE, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0.00833333333333333, check.thresholdRank = 0, check.quantileAtRatio = 1.44390094359269, check.quantileAtRank = NaN, isUniform = TRUE, clusterSize = 353
cluster 01_0000 is uniform

* checking uniformity of cluster '1' of 4 clusters
Asked to drop 0 genes and 879 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [321] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0501708984375 | max: 14.515625 | % negative: 8.5
Only analysis elapsed time: 3.58222031593323
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: 3.53522801399231
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0189824104309082
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0348601341247559
Estimating genes' coex
Calculate genes' coex elapsed time: 1.11781430244446
Total calculations elapsed time: 4.70688486099243
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.84228277206421
Total elapsed time: 11.6210660934448
Checking uniformity for the cluster '01_0001' with 321 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0001, with size 321, is uniform
Cluster 01_0001's shift to uniformity: -0.029501740796507
class = SimpleGDIUniformityCheck, check.isCheckAbove = FALSE, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0.005, check.thresholdRank = 0, check.quantileAtRatio = 1.43049825920349, check.quantileAtRank = NaN, isUniform = TRUE, clusterSize = 321
cluster 01_0001 is uniform

* checking uniformity of cluster '2' of 4 clusters
Asked to drop 0 genes and 905 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [295] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.054443359375 | max: 104 | % negative: 36.5
Only analysis elapsed time: 3.61109209060669
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: 3.58480739593506
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0196642875671387
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0177404880523682
Estimating genes' coex
Calculate genes' coex elapsed time: 1.12363338470459
Total calculations elapsed time: 4.74584555625916
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.84259724617004
Total elapsed time: 11.7228693962097
Checking uniformity for the cluster '01_0002' with 295 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0002, with size 295, is uniform
Cluster 01_0002's shift to uniformity: -0.0675248136510593
class = SimpleGDIUniformityCheck, check.isCheckAbove = FALSE, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0, check.thresholdRank = 0, check.quantileAtRatio = 1.39247518634894, check.quantileAtRank = NaN, isUniform = TRUE, clusterSize = 295
cluster 01_0002 is uniform

* checking uniformity of cluster '3' of 4 clusters
Asked to drop 0 genes and 969 cells
Cotan analysis functions started
Asked to drop 1 genes and 0 cells
Genes/cells selection done: dropped [1] genes and [0] cells
Working on [599] genes and [231] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0662841796875 | max: 82.5 | % negative: 33.889816360601
Only analysis elapsed time: 3.50102686882019
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: 3.56522250175476
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0207996368408203
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0188524723052979
Estimating genes' coex
Calculate genes' coex elapsed time: 1.13117814064026
Total calculations elapsed time: 4.73605275154114
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.89931631088257
Total elapsed time: 11.6264431476593
Checking uniformity for the cluster '01_0003' with 231 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0003, with size 231, is uniform
Cluster 01_0003's shift to uniformity: -0.0869783653733069
class = SimpleGDIUniformityCheck, check.isCheckAbove = FALSE, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0, check.thresholdRank = 0, check.quantileAtRatio = 1.37302163462669, check.quantileAtRank = NaN, isUniform = TRUE, clusterSize = 231
cluster 01_0003 is uniform


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

Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1  ->  3, 2  ->  1, 3  ->  2, 4  ->  4
Creating cells' uniform clustering: DONE
Applied reordering to clusterization is:
1  ->  1, 2  ->  2, 3  ->  3, 4  ->  4
Asked to drop 0 genes and 905 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [295] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.054443359375 | max: 104 | % negative: 36.5
Only analysis elapsed time: 3.54391431808472
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: 3.50997114181519
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0191335678100586
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0174722671508789
Estimating genes' coex
Calculate genes' coex elapsed time: 1.11560082435608
Total calculations elapsed time: 4.6621778011322
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.78152799606323
Total elapsed time: 11.5670108795166
Checking uniformity for the cluster 'Cluster_2' with 295 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster Cluster_2, with size 295, is uniform
Cluster Cluster_2's shift to uniformity: -0.00560790972802239
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0416666666666667, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.29139209027198, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.035, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.34700400911787, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00833333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.39247518634894, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 5, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.42797622180141, isUniform = TRUE, clusterSize = 295
Differential Expression Analysis - START
* DEA on cluster '-1' with 50 cells
* DEA on cluster '1' with 321 cells
* DEA on cluster '2' with 245 cells
* DEA on cluster '3' with 353 cells
* DEA on cluster '4' with 231 cells

Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1  ->  2, 2  ->  1, 3  ->  4, 4  ->  3, -1  ->  -1
Applied reordering to clusterization is:
1  ->  2, 2  ->  3, 3  ->  1, 4  ->  4, -1  ->  -1
Creating cells' uniform clustering: START
In iteration 1 the number of cells to re-cluster is 1200 cells belonging to 0 clusters
Asked to drop no genes or cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 4.4919068813324
Cotan genes' coex estimation started
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.99886512756348
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0199265480041504
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0530266761779785
Estimating genes' coex
Calculate genes' coex elapsed time: 1.15129399299622
Total calculations elapsed time: 5.22311234474182
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.34100651741028
Total elapsed time: 13.0810513496399
Running genes' selection: START
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Included 186 genes with GDI below 1.3
Selected 600 genes using HGDI selector
Running genes' selection: DONE
Creating Seurat object: START
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
PC_ 1 
Positive:  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 
Negative:  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 
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-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 
Negative:  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 
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-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 
Negative:  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 
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 1200
Number of edges: 55489

Running Louvain algorithm with multilevel refinement...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5973
Number of communities: 4
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 0.8
Creating Seurat object: DONE
Using passed in clusterization
Creating PDF UMAP in file:  /home/biocbuild/tmp/RtmpnFtjLL/test/reclustering/pdf_umap_1.pdf
UMAP plot
Calculating UMAP: START
08:18:10 UMAP embedding parameters a = 0.9922 b = 1.112
08:18:10 Read 1200 rows and found 40 numeric columns
08:18:10 Using Annoy for neighbor search, n_neighbors = 30
08:18:10 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
08:18:10 Writing NN index file to temp file /home/biocbuild/tmp/RtmpnFtjLL/file159fb5889782a
08:18:10 Searching Annoy index using 1 thread, search_k = 3000
08:18:10 Annoy recall = 100%
08:18:11 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
08:18:14 Initializing from normalized Laplacian + noise (using RSpectra)
08:18:14 Commencing optimization for 500 epochs, with 42618 positive edges
08:18:14 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
08:18:17 Optimization finished
Calculating UMAP: DONE
UMAP plot
Calculating UMAP: START
08:18:17 UMAP embedding parameters a = 0.9922 b = 1.112
08:18:17 Read 1200 rows and found 40 numeric columns
08:18:17 Using Annoy for neighbor search, n_neighbors = 30
08:18:17 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
08:18:18 Writing NN index file to temp file /home/biocbuild/tmp/RtmpnFtjLL/file159fb73bd89fd
08:18:18 Searching Annoy index using 1 thread, search_k = 3000
08:18:18 Annoy recall = 100%
08:18:19 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
08:18:21 Initializing from normalized Laplacian + noise (using RSpectra)
08:18:21 Commencing optimization for 500 epochs, with 42618 positive edges
08:18:21 Using rng type: pcg
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
08:18:25 Optimization finished
Calculating UMAP: DONE
* checking uniformity of cluster '1' of 2 clusters
Asked to drop 0 genes and 600 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [600] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0386962890625 | max: 19.40625 | % negative: 6.5
Only analysis elapsed time: 3.83096957206726
Cotan genes' coex estimation started
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.72693109512329
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0194940567016602
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0378689765930176
Estimating genes' coex
Calculate genes' coex elapsed time: 1.13146495819092
Total calculations elapsed time: 4.91575908660889
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.05420732498169
Total elapsed time: 12.10688996315
Checking uniformity for the cluster '01_0001' with 600 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0001, with size 600, is uniform
Cluster 01_0001's shift to uniformity: -0.0122560838733174
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0383333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.38474391612668, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.035, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42418110276822, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00666666666666667, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.45338035249414, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 4, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.51521594648006, isUniform = TRUE, clusterSize = 600
cluster 01_0001 is uniform

* checking uniformity of cluster '2' of 2 clusters
Asked to drop 0 genes and 600 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [600] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.032958984375 | max: 10.0859375 | % negative: 3.66666666666667
Only analysis elapsed time: 3.83261823654175
Cotan genes' coex estimation started
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.74753570556641
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0194618701934814
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0426037311553955
Estimating genes' coex
Calculate genes' coex elapsed time: 1.12504839897156
Total calculations elapsed time: 4.93464970588684
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.05437064170837
Total elapsed time: 12.1858711242676
Checking uniformity for the cluster '01_0002' with 600 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0002, with size 600, is uniform
Cluster 01_0002's shift to uniformity: -0.020344550553357
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0366666666666667, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.37665544944664, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.0316666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42305229982216, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00333333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.4378313582807, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 2, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.50182972335853, isUniform = TRUE, clusterSize = 600
cluster 01_0002 is uniform


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

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

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

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

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

Log Fold Change Analysis - DONE
findClustersMarkers - DONE
[1] "Tested cluster: 1"
Asked to drop 0 genes and 879 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [321] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0501708984375 | max: 14.515625 | % negative: 8.5
Only analysis elapsed time: 3.70146656036377
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: 3.62106275558472
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0227487087249756
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0374722480773926
Estimating genes' coex
Calculate genes' coex elapsed time: 1.13315296173096
Total calculations elapsed time: 4.81443667411804
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.93607687950134
Total elapsed time: 11.8880155086517
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
[1] "Tested cluster: 4"
Asked to drop 0 genes and 969 cells
Cotan analysis functions started
Asked to drop 1 genes and 0 cells
Genes/cells selection done: dropped [1] genes and [0] cells
Working on [599] genes and [231] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0662841796875 | max: 82.5 | % negative: 33.889816360601
Only analysis elapsed time: 3.5243763923645
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: 3.57499098777771
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0223865509033203
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0201270580291748
Estimating genes' coex
Calculate genes' coex elapsed time: 1.14025139808655
Total calculations elapsed time: 4.75775599479675
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.91975545883179
Total elapsed time: 11.7188792228699
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Initializing `COTAN` meta-data
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Cotan genes' coex estimation not requested
Total elapsed time: 7.96701550483704
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix

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

Number of nodes: 1200
Number of edges: 55881

Running Louvain algorithm with multilevel refinement...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5915
Number of communities: 4
Elapsed time: 0 seconds
Clusterizations found: RNA_snn_res.0.8, seurat_clusters
Conditions found: orig.ident
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Cotan genes' coex estimation not requested
Total elapsed time: 7.91427707672119
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 4.59216451644897
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: 4.10636591911316
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0210380554199219
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0538463592529297
Estimating genes' coex
Calculate genes' coex elapsed time: 1.12903785705566
Total calculations elapsed time: 5.31028819084167
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.43294143676758
Total elapsed time: 13.2573211193085
Calculating gene co-expression space - START
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
calculating PValues: DONE
Number of selected secondary markers: 6
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 6
Number of rows (U set): 60
Calculating gene co-expression space - DONE
Calculating gene co-expression space - START
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
calculating PValues: DONE
Number of selected secondary markers: 109
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 109
Number of rows (U set): 60
Calculating gene co-expression space - DONE
Establishing gene clusters - START
Calculating gene co-expression space - START
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
calculating PValues: DONE
Number of selected secondary markers: 109
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 109
Number of rows (U set): 60
Calculating gene co-expression space - DONE
Establishing gene clusters - DONE
Initializing `COTAN` meta-data
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Cotan genes' coex estimation not requested
Total elapsed time: 8.08946871757507
Differential Expression Analysis - START
* DEA on cluster '1' with 353 cells
* DEA on cluster '2' with 221 cells
* DEA on cluster '3' with 315 cells
* DEA on cluster '4' with 311 cells

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

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

Differential Expression Analysis - DONE
Updating check results for the 0 already tested pairs to align to new checker
2 new clusters pairs to be tested for merging:
c("1", "2") c("3", "4")
*1_2-merge
Asked to drop 0 genes and 626 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [574] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0340576171875 | max: 10.4375 | % negative: 4.33333333333333
Only analysis elapsed time: 3.92644548416138
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: 3.74812793731689
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0207881927490234
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0433483123779297
Estimating genes' coex
Calculate genes' coex elapsed time: 1.13014769554138
Total calculations elapsed time: 4.94241213798523
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.06655287742615
Total elapsed time: 12.2857441902161
Checking uniformity for the cluster '1_2-merge' with 574 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 1_2-merge, with size 574, is not uniform
Cluster 1_2-merge's shift to uniformity: 0.0820221369127558
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.326666666666667, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.37902213691276, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.28, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.41724738266282, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.0333333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.42971854140312, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 20, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.5067755752749, isUniform = FALSE, clusterSize = 574
Clusters 1 and 2 cannot be merged
*3_4-merge
Asked to drop 0 genes and 574 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [626] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.03839111328125 | max: 17.40625 | % negative: 6.66666666666667
Only analysis elapsed time: 3.82829594612122
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: 3.7805163860321
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0203282833099365
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0395433902740479
Estimating genes' coex
Calculate genes' coex elapsed time: 1.12735915184021
Total calculations elapsed time: 4.9677472114563
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.11631321907043
Total elapsed time: 12.1693053245544
Checking uniformity for the cluster '3_4-merge' with 626 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 3_4-merge, with size 626, is not uniform
Cluster 3_4-merge's shift to uniformity: 0.0914611744346205
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.248333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.38846117443462, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.218333333333333, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42066795244751, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.0366666666666667, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.45442688129939, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 22, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.52592182249634, isUniform = FALSE, clusterSize = 626
Clusters 3 and 4 cannot be merged
Finished the first batch - no merges were executed
Start merging nearest clusters: iteration 2
Differential Expression Analysis - START
* DEA on cluster '1' with 353 cells
* DEA on cluster '2' with 221 cells
* DEA on cluster '3' with 315 cells
* DEA on cluster '4' with 311 cells

Differential Expression Analysis - DONE
Updating check results for the 2 already tested pairs to align to new checker
2 new clusters pairs to be tested for merging:
c("2", "3") c("2", "4")
*2_3-merge
Asked to drop 0 genes and 664 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [536] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0390625 | max: 12.59375 | % negative: 9.16666666666667
Only analysis elapsed time: 3.74558305740356
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: 3.71548247337341
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0193188190460205
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0290024280548096
Estimating genes' coex
Calculate genes' coex elapsed time: 1.12524104118347
Total calculations elapsed time: 4.88904476165771
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.03073954582214
Total elapsed time: 12.0610914230347
Checking uniformity for the cluster '2_3-merge' with 536 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 2_3-merge, with size 536, is not uniform
Cluster 2_3-merge's shift to uniformity: 0.102213698003784
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.29, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.39921369800378, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.251666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.45276697088287, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.05, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.49016449535422, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 30, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.54477108741148, isUniform = FALSE, clusterSize = 536
Clusters 2 and 3 cannot be merged
*2_4-merge
Asked to drop 0 genes and 668 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [532] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.04754638671875 | max: 10.234375 | % negative: 5
Only analysis elapsed time: 3.95919799804688
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: 3.84508562088013
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0216653347015381
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0410113334655762
Estimating genes' coex
Calculate genes' coex elapsed time: 1.15578150749207
Total calculations elapsed time: 5.06354379653931
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.22563171386719
Total elapsed time: 12.5203905105591
Checking uniformity for the cluster '2_4-merge' with 532 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 2_4-merge, with size 532, is not uniform
Cluster 2_4-merge's shift to uniformity: 0.213129217682233
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.39, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.51012921768223, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.361666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.55599610798341, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.181666666666667, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.59088431608469, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 109, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.68475283375668, isUniform = FALSE, clusterSize = 532
Clusters 2 and 4 cannot be merged
No clusters will be merged
None of the remaining tested cluster pairs could be merged
Executed all merges for threshold 1.297 out of 4 checks
Start merging nearest clusters - the main threshold is: 1.397
Start merging nearest clusters: iteration 3
Differential Expression Analysis - START
* DEA on cluster '1' with 353 cells
* DEA on cluster '2' with 221 cells
* DEA on cluster '3' with 315 cells
* DEA on cluster '4' with 311 cells

Differential Expression Analysis - DONE
Updating check results for the 4 already tested pairs to align to new checker
2 new clusters pairs to be tested for merging:
c("1", "3") c("1", "4")
*1_3-merge
Asked to drop 0 genes and 532 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [668] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.046630859375 | max: 9.03515625 | % negative: 1.33333333333333
Only analysis elapsed time: 4.05221843719482
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: 3.74287891387939
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0191173553466797
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0422923564910889
Estimating genes' coex
Calculate genes' coex elapsed time: 1.11840677261353
Total calculations elapsed time: 4.92269539833069
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.04352593421936
Total elapsed time: 12.3921325206757
Checking uniformity for the cluster '1_3-merge' with 668 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 1_3-merge, with size 668, is not uniform
Cluster 1_3-merge's shift to uniformity: 0.177923707405291
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.33, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.57492370740529, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.31, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.6368755707341, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.128333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.65704996173771, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 77, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.68881338289976, isUniform = FALSE, clusterSize = 668
Clusters 1 and 3 cannot be merged
*1_4-merge
Asked to drop 0 genes and 536 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [664] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0164794921875 | max: 5.5595703125 | % negative: 0.166666666666667
Only analysis elapsed time: 4.06129670143127
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: 3.81850218772888
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0211982727050781
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0503058433532715
Estimating genes' coex
Calculate genes' coex elapsed time: 1.15703749656677
Total calculations elapsed time: 5.047043800354
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.19043612480164
Total elapsed time: 12.5253231525421
Checking uniformity for the cluster '1_4-merge' with 664 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 1_4-merge, with size 664, is not uniform
Cluster 1_4-merge's shift to uniformity: 0.138277355686155
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.348333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.53527735568615, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.316666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.55951216335001, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.0983333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.5910569684761, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 59, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.64605433203112, isUniform = FALSE, clusterSize = 664
Clusters 1 and 4 cannot be merged
Clusters 2 and 1 will be merged
Clusters 3 and 4 will be merged
Executed 2 merges
Start merging nearest clusters: iteration 4
Differential Expression Analysis - START
* DEA on cluster '1_2-merge' with 574 cells
* DEA on cluster '3_4-merge' with 626 cells

Differential Expression Analysis - DONE
Updating check results for the 6 already tested pairs to align to new checker
1 new clusters pairs to be tested for merging:
c("1_2-merge", "3_4-merge")
*1_2-merge_3_4-merge-merge
Asked to drop no genes or cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 4.74990081787109
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: 4.21432590484619
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0203783512115479
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0531117916107178
Estimating genes' coex
Calculate genes' coex elapsed time: 1.17344856262207
Total calculations elapsed time: 5.46126461029053
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.63824391365051
Total elapsed time: 13.7130093574524
Checking uniformity for the cluster '1_2-merge_3_4-merge-merge' with 1200 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 1_2-merge_3_4-merge-merge, with size 1200, is not uniform
Cluster 1_2-merge_3_4-merge-merge's shift to uniformity: 0.173174985379327
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.415, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.57017498537933, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.388333333333333, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.61240081401504, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.15, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.64046660675367, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 90, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.66512085964759, isUniform = FALSE, clusterSize = 1200
Clusters 1_2-merge and 3_4-merge cannot be merged
No clusters will be merged
None of the remaining tested cluster pairs could be merged
Executed all merges for threshold 1.397 out of 7 checks
The final merged clusterization contains [2] different clusters: 1_2-merge, 3_4-merge
Differential Expression Analysis - START
* DEA on cluster '1' with 574 cells
* DEA on cluster '2' with 626 cells

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

Log Fold Change Analysis - DONE
Asked to drop 0 genes and 626 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [574] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.0340576171875 | max: 10.4375 | % negative: 4.33333333333333
Only analysis elapsed time: 3.85085988044739
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: 3.67215609550476
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0212326049804688
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.044074535369873
Estimating genes' coex
Calculate genes' coex elapsed time: 1.12512922286987
Total calculations elapsed time: 4.86259245872498
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 5.96537971496582
Total elapsed time: 12.1117718219757
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
Asked to drop 0 genes and 574 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [626] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
`dispersion` | min: -0.03839111328125 | max: 17.40625 | % negative: 6.66666666666667
Only analysis elapsed time: 3.94550943374634
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: 3.75630259513855
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0217485427856445
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0422072410583496
Estimating genes' coex
Calculate genes' coex elapsed time: 1.14810919761658
Total calculations elapsed time: 4.96836757659912
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 6.11731338500977
Total elapsed time: 12.2840847969055
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Calculate `GDI`: DONE
Calculate GDI dataframe: DONE
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 562 ]
> 
> proc.time()
   user  system elapsed 
970.260   5.075 970.149

Example timings

COTAN.Rcheck/COTAN-Ex.timings

name	user	system	elapsed
COTAN_Legacy	0.000	0.002	0.003
COTAN_ObjectCreation	13.787	1.475	14.744
CalculatingCOEX	73.777	0.236	71.592
ClustersList	0.011	0.000	0.010
Conversions	7.854	0.028	7.897
GenesStatistics	15.261	0.043	14.827
HandleMetaData	0.105	0.000	0.105
HandlingClusterizations	58.176	0.159	57.848
HandlingConditions	0.151	0.000	0.151
HeatmapPlots	47.845	0.283	46.482
LoggingFunctions	0.002	0.000	0.003
ParametersEstimations	34.354	0.208	34.632
RawDataCleaning	7.181	0.015	7.219
RawDataGetters	0.092	0.009	0.100
UniformClusters	250.703	0.709	249.103
getColorsVector	0.001	0.000	0.002