Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-18 12:04 -0400 (Mon, 18 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4596 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4538 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
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 |
Package 449/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
COTAN 2.9.5 (landing page) Galfrè Silvia Giulia
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
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. |
Package: COTAN |
Version: 2.9.5 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:COTAN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings COTAN_2.9.5.tar.gz |
StartedAt: 2025-08-17 19:58:48 -0400 (Sun, 17 Aug 2025) |
EndedAt: 2025-08-17 20:24:50 -0400 (Sun, 17 Aug 2025) |
EllapsedTime: 1562.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: COTAN.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:COTAN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings COTAN_2.9.5.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/COTAN.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘COTAN/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘COTAN’ version ‘2.9.5’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 26 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed UniformClusters 206.733 3.124 209.496 CalculatingCOEX 58.306 1.154 59.707 HandlingClusterizations 42.845 1.226 43.684 HeatmapPlots 35.686 0.938 36.852 ParametersEstimations 25.977 0.791 26.882 GenesStatistics 12.280 0.388 12.532 COTAN_ObjectCreation 12.158 0.326 12.571 Conversions 6.270 0.136 6.447 RawDataCleaning 4.823 0.300 4.944 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘outputTestDatasetCreation.R’ Running ‘spelling.R’ Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
COTAN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL COTAN ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘COTAN’ ... ** this is package ‘COTAN’ version ‘2.9.5’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (COTAN)
COTAN.Rcheck/tests/outputTestDatasetCreation.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > > # Creates the files to be reloaded by the tests for comparisons > library(zeallot) > > outputTestDatasetCreation <- function(testsDir = file.path("tests", + "testthat")) { + utils::data("test.dataset", package = "COTAN") + options(parallelly.fork.enable = TRUE) + + obj <- COTAN(raw = test.dataset) + obj <- initializeMetaDataset(obj, GEO = " ", + sequencingMethod = "artificial", + sampleCondition = "test") + + obj <- proceedToCoex(obj, cores = 6L, saveObj = FALSE) + #saveRDS(obj, file = file.path(testsDir,"temp.RDS")) + + cells.names.test <- getCells(obj)[c(1L:10L, 591L:610L, 991L:1000L)] + genes.names.test <- getGenes(obj)[c(1L:10L, 291L:310L, 591L: 600L)] + saveRDS(cells.names.test, file.path(testsDir, "cells.names.test.RDS")) + saveRDS(genes.names.test, file.path(testsDir, "genes.names.test.RDS")) + + dispersion.test <- getDispersion(obj)[genes.names.test] + saveRDS(dispersion.test, file.path(testsDir, "dispersion.test.RDS")) + + raw.norm.test <- getNuNormData(obj)[genes.names.test, cells.names.test] + saveRDS(raw.norm.test, file.path(testsDir, "raw.norm.test.RDS")) + + coex.test <- getGenesCoex(obj, genes = genes.names.test, zeroDiagonal = FALSE) + saveRDS(coex.test, file.path(testsDir, "coex.test.RDS")) + + lambda.test <- getLambda(obj)[genes.names.test] + saveRDS(lambda.test, file.path(testsDir, "lambda.test.RDS")) + + GDI.test <- calculateGDI(obj) + GDI.test <- GDI.test[genes.names.test, ] + saveRDS(GDI.test, file.path(testsDir, "GDI.test.RDS")) + + nu.test <- getNu(obj)[cells.names.test] + saveRDS(nu.test, file.path(testsDir, "nu.test.RDS")) + + pval.test <- calculatePValue(obj, geneSubsetCol = genes.names.test) + saveRDS(pval.test, file.path(testsDir, "pval.test.RDS")) + + GDIThreshold <- 1.46 + initialResolution <- 0.8 + clusters <- cellsUniformClustering(obj, GDIThreshold = GDIThreshold, + initialResolution = initialResolution, + cores = 6L, saveObj = FALSE)[["clusters"]] + saveRDS(clusters, file.path(testsDir, "clusters1.RDS")) + + coexDF <- DEAOnClusters(obj, clusters = clusters) + obj <- addClusterization(obj, clName = "clusters", + clusters = clusters, coexDF = coexDF) + + saveRDS(coexDF[genes.names.test, ], + file.path(testsDir, "coex.test.cluster1.RDS")) + + pvalDF <- pValueFromDEA(coexDF, getNumCells(obj), adjustmentMethod = "none") + + saveRDS(pvalDF[genes.names.test, ], + file.path(testsDir, "pval.test.cluster1.RDS")) + + c(mergedClusters, mCoexDF) %<-% + mergeUniformCellsClusters(objCOTAN = obj, + clusters = NULL, + GDIThreshold = GDIThreshold, + cores = 6L, + distance = "cosine", + hclustMethod = "ward.D2", + saveObj = FALSE) + + saveRDS(mergedClusters[genes.names.test], + file.path(testsDir, "cluster_data_merged.RDS")) + } > > proc.time() user system elapsed 0.209 0.076 0.271
COTAN.Rcheck/tests/spelling.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > if (requireNamespace("spelling", quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) NULL > > proc.time() user system elapsed 0.192 0.072 0.262
COTAN.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > Sys.setenv(R_TESTS = "") > library(testthat) > library(COTAN) > test_check("COTAN") Setting new log level to 4 Initializing `COTAN` meta-data Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: 0.9033203125 | max: 4.6796875 | % negative: 10 Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.38960194587708 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00117301940917969 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00623297691345215 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.836664915084839 Total calculations elapsed time: 3.23367285728455 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: 2.58435106277466 Calculating genes' COEX normalization factor Fraction of genes' with very low expected contingency tables: 0.181818181818182 Calculate genes' normalization factor elapsed time: 0.000683069229125977 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00424098968505859 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.944697856903076 Total calculations elapsed time: 3.53397297859192 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: 2.66585779190063 Calculating cells' COEX normalization factor Fraction of cells' with very low expected contingency tables: 0 Calculate cells' normalization factor elapsed time: 0.00131511688232422 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00301504135131836 Estimating cells' COEX Calculate cells' COEX elapsed time: 0.872876882553101 Total calculations elapsed time: 3.54306483268738 Calculate cells' COEX (legacy): DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE Included 1 genes with GDI below 1.3 Selected 10 genes using HGDI selector Running genes' selection: DONE Running genes' selection: START Included 1 genes with GDI below 1.3 Selected 10 genes using HGDI selector Running genes' selection: DONE Running genes' selection: START Included 1 genes with GDI below 1.3 Selected 10 genes using HGDI selector Running genes' selection: DONE Running genes' selection: START Selected 5 genes using HGDI selector Running genes' selection: DONE Running genes' selection: START Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer counts Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Selected 5 genes using HVG_Seurat selector Running genes' selection: DONE Running genes' selection: START Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer data Calculating gene means 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variance to mean ratios 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Running genes' selection: START Given 5 genes as input Running genes' selection: DONE Elaborating Reduced dimensionality Data Matrix - START Running genes' selection: START Included 1 genes with GDI below 1.3 Selected 10 genes using HGDI selector Running genes' selection: DONE Elaborating PCA - START Elaborating PCA - DONE Elaborating Reduced dimensionality Data Matrix - DONE Elaborating Reduced dimensionality Data Matrix - START Running genes' selection: START Included 1 genes with GDI below 1.3 Selected 10 genes using HGDI selector Running genes' selection: DONE Elaborating PCA - START Elaborating PCA - DONE Elaborating Reduced dimensionality Data Matrix - DONE Elaborating Reduced dimensionality Data Matrix - START Running genes' selection: START Selected 8 genes using HGDI selector Running genes' selection: DONE Elaborating PCA - START Elaborating PCA - DONE Elaborating Reduced dimensionality Data Matrix - DONE Elaborating Reduced dimensionality Data Matrix - START Running genes' selection: START Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer counts Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Selected 8 genes using HVG_Seurat selector Running genes' selection: DONE Elaborating PCA - START Elaborating PCA - DONE Elaborating Reduced dimensionality Data Matrix - DONE Elaborating Reduced dimensionality Data Matrix - START Elaborating COEX Eigen Vectors - START Elaborating COEX Eigen Vectors - DONE Elaborating Reduced dimensionality Data Matrix - DONE Elaborating Reduced dimensionality Data Matrix - START Elaborating COEX Eigen Vectors - START Elaborating COEX Eigen Vectors - DONE Elaborating Reduced dimensionality Data Matrix - DONE Initializing `COTAN` meta-data Initializing `COTAN` meta-data Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate `dispersion`/`nu`: START Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: 0.903564453125 | max: 4.679443359375 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Estimate `nu`: DONE `nu` change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014 `nu` mean: 1.68489292689732 Marginal errors | max: 1.73564890252257 | median 1.37996360874076 | mean: 1.32180348113228 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: 0.0655517578125 | max: 3.5439453125 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Estimate `nu`: DONE `nu` change (abs) | max: 0.402649984216273 | median: 0.231868788425666 | mean: 0.231868788425666 `nu` mean: 0.829218804209393 Marginal errors | max: 0.80321315986594 | median 0.677497553540581 | mean: 0.619375430892821 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: 0.3260498046875 | max: 4.026123046875 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Estimate `nu`: DONE `nu` change (abs) | max: 0.158004893526231 | median: 0.0919692884670312 | mean: 0.0919692884670312 `nu` mean: 1.0660356050592 Marginal errors | max: 0.250724014302326 | median 0.206232152124436 | mean: 0.190425623677198 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: 0.23040771484375 | max: 3.8736572265625 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Estimate `nu`: DONE `nu` change (abs) | max: 0.0532774732102337 | median: 0.0308837890624999 | mean: 0.0308837890624999 `nu` mean: 0.977606315852266 Marginal errors | max: 0.0916983669060123 | median 0.0765266929824948 | mean: 0.0697593208689684 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: 0.26348876953125 | max: 3.928955078125 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Estimate `nu`: DONE `nu` change (abs) | max: 0.0189966206463044 | median: 0.0110199320575908 | mean: 0.0110199320575908 `nu` mean: 1.00797668858871 Marginal errors | max: 0.0317151207459254 | median 0.0262702142278251 | mean: 0.0240886952086962 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: 0.2518310546875 | max: 3.9097900390625 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Estimate `nu`: DONE `nu` change (abs) | max: 0.00670088501353994 | median: 0.00388888101583662 | mean: 0.00388888101583662 `nu` mean: 0.997187996002297 Marginal errors | max: 0.0113693316356223 | median 0.00939669372836249 | mean: 0.00860715734056932 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: 0.2559814453125 | max: 3.9166259765625 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Estimate `nu`: DONE `nu` change (abs) | max: 0.00251007446998996 | median: 0.00144735987374958 | mean: 0.00144735987374958 `nu` mean: 1.00106271459624 Marginal errors | max: 0.00406746973787442 | median 0.00343393462175534 | mean: 0.00313496757119527 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: 0.25445556640625 | max: 3.9140625 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Estimate `nu`: DONE `nu` change (abs) | max: 0.000837027590858019 | median: 0.000488281249999889 | mean: 0.000488281249999889 `nu` mean: 0.999651253659142 Marginal errors | max: 0.00143433714371533 | median 0.00116636244706747 | mean: 0.00109289166947839 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: 0.2550048828125 | max: 3.9150390625 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Estimate `nu`: DONE `nu` change (abs) | max: 0.000209227688885871 | median: 0.0001220703125 | mean: 0.0001220703125 `nu` mean: 1.00008715737639 Marginal errors | max: 0.000379524846207957 | median 0.000325685250686547 | mean: 0.000295532844332236 Estimate `dispersion`/`nu`: DONE While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.60024499893188 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.000474929809570312 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00124716758728027 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.870348930358887 Total calculations elapsed time: 3.47231602668762 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: 2.68166494369507 Calculating cells' COEX normalization factor Calculate cells' normalization factor elapsed time: 0.000791072845458984 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00197601318359375 Estimating cells' COEX Calculate cells' COEX elapsed time: 0.901565790176392 Total calculations elapsed time: 3.58599781990051 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: 2.69356799125671 Calculating genes' COEX normalization factor Fraction of genes' with very low expected contingency tables: 0.181818181818182 Calculate genes' normalization factor elapsed time: 0.000668048858642578 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00132393836975098 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.895117998123169 Total calculations elapsed time: 3.59067797660828 Calculate genes' COEX (legacy): DONE While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.79681706428528 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.000540018081665039 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00133204460144043 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.973489999771118 Total calculations elapsed time: 3.7721791267395 Calculate genes' COEX (legacy): DONE Calculate genes' partial COEX: START Retrieving expected genes' partial contingency table calculating partial NN.. done calculating partial NY..YN..YY.. done Calculating genes' partial COEX normalization factor Fraction of genes with very low expected contingency tables: 0.1 Retrieving observed genes' yes/yes partial contingency table calculating partial YY.. done Estimating genes' partial COEX Calculate genes' partial COEX: DONE Calculate genes' partial COEX: START Retrieving expected genes' partial contingency table calculating partial NN.. done calculating partial NY..YN..YY.. done Calculating genes' partial COEX normalization factor Fraction of genes with very low expected contingency tables: 0.4 Retrieving observed genes' yes/yes partial contingency table calculating partial YY.. done Estimating genes' partial COEX Calculate genes' partial COEX: DONE Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells calculating YY.. done calculating YY.. done calculating NY..YN..NN..t().. done Estimate `dispersion`/`nu`: START Estimate `dispersion`: START Effective number of cores used: 1 Executing 3 genes batches `dispersion` | min: 0.903564453125 | max: 4.679443359375 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 5 cells batches Estimate `nu`: DONE `nu` change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014 `nu` mean: 1.68489292689732 Marginal errors | max: 0.25535328937316 | median 0.0807577993228135 | mean: 0.101980750205762 Estimate `dispersion`: START Effective number of cores used: 1 Executing 3 genes batches `dispersion` | min: 1.037109375 | max: 4.6107177734375 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 5 cells batches Estimate `nu`: DONE `nu` change (abs) | max: 0.0273438105507502 | median: 0.0148852611818011 | mean: 0.0148852611818011 `nu` mean: 1.69735147626627 Marginal errors | max: 0.00326864580272002 | median 0.00111524657842743 | mean: 0.00131556083122533 Estimate `dispersion`: START Effective number of cores used: 1 Executing 3 genes batches `dispersion` | min: 1.03887939453125 | max: 4.6097412109375 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 5 cells batches Estimate `nu`: DONE `nu` change (abs) | max: 0 | median: 0 | mean: 0 `nu` mean: 1.69735147626627 Marginal errors | max: 7.56328383637594e-05 | median 1.72948087246994e-05 | mean: 2.99252342145451e-05 Estimate `dispersion`/`nu`: DONE calculating NN.. done calculating NN.. done calculating YN..NY..YY..t().. done Calculate cells' COEX (legacy): START Retrieving expected cells' contingency table calculating NN.. done calculating YN..NY..YY..t().. done Expected cells' contingency table elapsed time: 2.74396204948425 Calculating cells' COEX normalization factor Fraction of cells' with very low expected contingency tables: 0 Calculate cells' normalization factor elapsed time: 0.000658988952636719 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00153493881225586 Estimating cells' COEX Calculate cells' COEX elapsed time: 0.909533023834229 Total calculations elapsed time: 3.65568900108337 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: 2.66335082054138 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.000524044036865234 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00131797790527344 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.872799158096313 Total calculations elapsed time: 3.53799200057983 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: 3.54092907905579 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: 3.4162290096283 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0101830959320068 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0512218475341797 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.903712034225464 Total calculations elapsed time: 4.38134598731995 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.25973200798035 Total elapsed time: 10.5474328994751 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: 3.45366096496582 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: 3.35513401031494 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0101380348205566 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0491018295288086 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.862003087997437 Total calculations elapsed time: 4.27637696266174 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.16728210449219 Total elapsed time: 10.4700980186462 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: 3.59952902793884 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: 3.44686818122864 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0080718994140625 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0453910827636719 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.942055940628052 Total calculations elapsed time: 4.44238710403442 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.41334390640259 Total elapsed time: 10.8577868938446 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: 3.49564814567566 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: 3.34756588935852 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00749707221984863 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0490329265594482 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.930554151535034 Total calculations elapsed time: 4.33465003967285 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.25279688835144 Total elapsed time: 10.650955915451 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: 5.58060598373413 Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.81571507453918 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00664901733398438 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00618982315063477 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.909836053848267 Total calculations elapsed time: 3.73838996887207 Calculate genes' COEX (legacy): DONE While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.85593199729919 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00614094734191895 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00679206848144531 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.895092010498047 Total calculations elapsed time: 3.76395702362061 Calculate genes' COEX (legacy): DONE While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.68855500221252 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00707197189331055 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00605487823486328 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.932153940200806 Total calculations elapsed time: 3.6338357925415 Calculate genes' COEX (legacy): DONE Hangling COTAN object with condition: test Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and on a set of genes on rows calculating PValues: DONE Handling genes type: G2 Handling genes type: G3 Initializing `COTAN` meta-data Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells PCA: START Elaborating PCA - START Elaborating PCA - DONE PCA: DONE Hierarchical clustering: START Hierarchical clustering: DONE Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Only analysis elapsed time: 3.5055239200592 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: 3.41979694366455 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00720405578613281 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0460708141326904 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.944658041000366 Total calculations elapsed time: 4.41772985458374 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.41645693778992 Total elapsed time: 13.8476169109344 Saving elaborated data locally at: /tmp/Rtmpf4IFEu/test.cotan.RDS Creating new clusterization: START Elaborating Reduced dimensionality Data Matrix - START Elaborating COEX Eigen Vectors - START Elaborating COEX Eigen Vectors - DONE Elaborating Reduced dimensionality Data Matrix - DONE Computing nearest neighbor graph Computing SNN Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 1200 Number of edges: 37723 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.5827 Number of communities: 2 Elapsed time: 0 seconds Number of clusters is too small. Reclustering at resolution higher than: 0.8 Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 1200 Number of edges: 37723 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.3954 Number of communities: 5 Elapsed time: 0 seconds Used resolution for Seurat clusterization is: 1.3 Creating new clusterization: DONE Creating cells' uniform clustering: START In iteration 1 the number of cells to re-cluster is 1200 cells belonging to 0 clusters Asked to drop no genes or cells Creating new clusterization: START Elaborating Reduced dimensionality Data Matrix - START Running genes' selection: START Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer counts Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Selected 600 genes using HVG_Seurat selector Running genes' selection: DONE Elaborating PCA - START Elaborating PCA - DONE Elaborating Reduced dimensionality Data Matrix - DONE Computing nearest neighbor graph Computing SNN Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 1200 Number of edges: 55489 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.5973 Number of communities: 4 Elapsed time: 0 seconds Used resolution for Seurat clusterization is: 0.8 Creating new clusterization: DONE Creating PDF UMAP in file: /tmp/Rtmpf4IFEu/test/reclustering/pdf_umap_1.pdf UMAP plot Calculating UMAP: START 20:18:04 UMAP embedding parameters a = 0.9922 b = 1.112 20:18:04 Read 1200 rows and found 40 numeric columns 20:18:04 Using Annoy for neighbor search, n_neighbors = 30 20:18:04 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 20:18:04 Writing NN index file to temp file /tmp/Rtmpf4IFEu/filea530e8f9b23 20:18:04 Searching Annoy index using 1 thread, search_k = 3000 20:18:04 Annoy recall = 100% 20:18:05 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 20:18:07 Initializing from normalized Laplacian + noise (using RSpectra) 20:18:07 Commencing optimization for 500 epochs, with 42674 positive edges 20:18:07 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 20:18:10 Optimization finished Calculating UMAP: DONE UMAP plot Calculating UMAP: START 20:18:10 UMAP embedding parameters a = 0.9922 b = 1.112 20:18:10 Read 1200 rows and found 40 numeric columns 20:18:10 Using Annoy for neighbor search, n_neighbors = 30 20:18:10 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 20:18:10 Writing NN index file to temp file /tmp/Rtmpf4IFEu/filea5301f834c23 20:18:10 Searching Annoy index using 1 thread, search_k = 3000 20:18:10 Annoy recall = 100% 20:18:11 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 20:18:13 Initializing from normalized Laplacian + noise (using RSpectra) 20:18:13 Commencing optimization for 500 epochs, with 42674 positive edges 20:18:13 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 20:18:16 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: 3.15063500404358 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: 3.12973189353943 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00861716270446777 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0338759422302246 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.941123008728027 Total calculations elapsed time: 4.11334800720215 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.0824990272522 Total elapsed time: 10.1734108924866 Checking uniformity for the cluster '01_0000' with 353 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0000, with size 353, is uniform Cluster 01_0000's shift to uniformity: -0.0160990564073067 class = SimpleGDIUniformityCheck, check.isCheckAbove = FALSE, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0.00833333333333333, check.thresholdRank = 0, check.quantileAtRatio = 1.44390094359269, check.quantileAtRank = NaN, isUniform = TRUE, clusterSize = 353 cluster 01_0000 is uniform * checking uniformity of cluster '1' of 4 clusters Asked to drop 0 genes and 879 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [321] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: -0.0501708984375 | max: 14.515625 | % negative: 8.5 Only analysis elapsed time: 2.96506881713867 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: 3.11487889289856 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00620317459106445 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0328128337860107 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.937739133834839 Total calculations elapsed time: 4.09163403511047 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.07695508003235 Total elapsed time: 10.0388998985291 Checking uniformity for the cluster '01_0001' with 321 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0001, with size 321, is uniform Cluster 01_0001's shift to uniformity: -0.029501740796509 class = SimpleGDIUniformityCheck, check.isCheckAbove = FALSE, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0.005, check.thresholdRank = 0, check.quantileAtRatio = 1.43049825920349, check.quantileAtRank = NaN, isUniform = TRUE, clusterSize = 321 cluster 01_0001 is uniform * checking uniformity of cluster '2' of 4 clusters Asked to drop 0 genes and 905 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [295] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: -0.054443359375 | max: 104 | % negative: 36.5 Only analysis elapsed time: 3.2375659942627 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: 3.26735901832581 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00833392143249512 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0137960910797119 Estimating genes' COEX Calculate genes' COEX elapsed time: 1.01328301429749 Total calculations elapsed time: 4.3027720451355 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.30156207084656 Total elapsed time: 10.5800359249115 Checking uniformity for the cluster '01_0002' with 295 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0002, with size 295, is uniform Cluster 01_0002's shift to uniformity: -0.0675248136510636 class = SimpleGDIUniformityCheck, check.isCheckAbove = FALSE, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0, check.thresholdRank = 0, check.quantileAtRatio = 1.39247518634894, check.quantileAtRank = NaN, isUniform = TRUE, clusterSize = 295 cluster 01_0002 is uniform * checking uniformity of cluster '3' of 4 clusters Asked to drop 0 genes and 969 cells Cotan analysis functions started Asked to drop 1 genes and 0 cells Genes/cells selection done: dropped [1] genes and [0] cells Working on [599] genes and [231] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: -0.0662841796875 | max: 82.5 | % negative: 33.889816360601 Only analysis elapsed time: 3.01050496101379 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: 3.08980917930603 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00611782073974609 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0178210735321045 Estimating genes' COEX Calculate genes' COEX elapsed time: 1.00541400909424 Total calculations elapsed time: 4.11916208267212 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.13160490989685 Total elapsed time: 10.0502038002014 Checking uniformity for the cluster '01_0003' with 231 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0003, with size 231, is uniform Cluster 01_0003's shift to uniformity: -0.0869783653733054 class = SimpleGDIUniformityCheck, check.isCheckAbove = FALSE, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0, check.thresholdRank = 0, check.quantileAtRatio = 1.37302163462669, check.quantileAtRank = NaN, isUniform = TRUE, clusterSize = 231 cluster 01_0003 is uniform Found 4 uniform and 0 non-uniform clusters Stopping: too few cells left to cluster Unclustered cell left: 0 The final raw clusterization contains [ 4 ] different clusters: 01_0000, 01_0001, 01_0002, 01_0003 Differential Expression Analysis - START * DEA on cluster '1' with 353 cells * DEA on cluster '2' with 321 cells * DEA on cluster '3' with 295 cells * DEA on cluster '4' with 231 cells Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 3, 2 -> 1, 3 -> 2, 4 -> 4 Creating cells' uniform clustering: DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2, 3 -> 3, 4 -> 4 Asked to drop 0 genes and 905 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [295] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: -0.054443359375 | max: 104 | % negative: 36.5 Only analysis elapsed time: 3.01781392097473 Cotan genes' COEX estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' COEX (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 5.68507099151611 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.0149481296539307 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0225028991699219 Estimating genes' COEX Calculate genes' COEX elapsed time: 1.41960406303406 Total calculations elapsed time: 7.14212608337402 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 8.09744000434875 Total elapsed time: 12.9814040660858 Checking uniformity for the cluster 'Cluster_2' with 295 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster Cluster_2, with size 295, is uniform Cluster Cluster_2's shift to uniformity: -0.00560790972802017 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0416666666666667, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.29139209027198, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.035, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.34700400911787, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00833333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.39247518634894, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 5, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.4279762218014, isUniform = TRUE, clusterSize = 295 Differential Expression Analysis - START * DEA on cluster '-1' with 50 cells * DEA on cluster '1' with 321 cells * DEA on cluster '2' with 245 cells * DEA on cluster '3' with 353 cells * DEA on cluster '4' with 231 cells Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 2, 2 -> 1, 3 -> 4, 4 -> 3, -1 -> -1 Applied reordering to clusterization is: 1 -> 2, 2 -> 3, 3 -> 1, 4 -> 4, -1 -> -1 Creating cells' uniform clustering: START In iteration 1 the number of cells to re-cluster is 1200 cells belonging to 0 clusters Asked to drop no genes or cells Creating new clusterization: START Elaborating Reduced dimensionality Data Matrix - START Running genes' selection: START Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE Included 186 genes with GDI below 1.3 Selected 600 genes using HGDI selector Running genes' selection: DONE Elaborating PCA - START Elaborating PCA - DONE Elaborating Reduced dimensionality Data Matrix - DONE Computing nearest neighbor graph Computing SNN Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 1200 Number of edges: 55489 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.5973 Number of communities: 4 Elapsed time: 0 seconds Used resolution for Seurat clusterization is: 0.8 Creating new clusterization: DONE Using passed in clusterization Creating PDF UMAP in file: /tmp/Rtmpf4IFEu/test/reclustering/pdf_umap_1.pdf UMAP plot Calculating UMAP: START 20:19:51 UMAP embedding parameters a = 0.9922 b = 1.112 20:19:51 Read 1200 rows and found 40 numeric columns 20:19:51 Using Annoy for neighbor search, n_neighbors = 30 20:19:51 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 20:19:52 Writing NN index file to temp file /tmp/Rtmpf4IFEu/filea5307a6bcfe7 20:19:52 Searching Annoy index using 1 thread, search_k = 3000 20:19:52 Annoy recall = 100% 20:19:53 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 20:19:55 Initializing from normalized Laplacian + noise (using RSpectra) 20:19:55 Commencing optimization for 500 epochs, with 42644 positive edges 20:19:55 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 20:20:01 Optimization finished Calculating UMAP: DONE UMAP plot Calculating UMAP: START 20:20:01 UMAP embedding parameters a = 0.9922 b = 1.112 20:20:01 Read 1200 rows and found 40 numeric columns 20:20:01 Using Annoy for neighbor search, n_neighbors = 30 20:20:01 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 20:20:01 Writing NN index file to temp file /tmp/Rtmpf4IFEu/filea53077cd6d12 20:20:01 Searching Annoy index using 1 thread, search_k = 3000 20:20:02 Annoy recall = 100% 20:20:02 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 20:20:04 Initializing from normalized Laplacian + noise (using RSpectra) 20:20:04 Commencing optimization for 500 epochs, with 42644 positive edges 20:20:04 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 20:20:07 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: 3.17332100868225 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: 3.18290090560913 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00945401191711426 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0328769683837891 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.954434156417847 Total calculations elapsed time: 4.17966604232788 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.11331295967102 Total elapsed time: 10.1303470134735 Checking uniformity for the cluster '01_0001' with 600 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0001, with size 600, is uniform Cluster 01_0001's shift to uniformity: -0.012256083873327 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0383333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.38474391612667, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.035, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42418110276821, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00666666666666667, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.45338035249414, 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 = 1.51521594648007, isUniform = TRUE, clusterSize = 600 cluster 01_0001 is uniform * checking uniformity of cluster '2' of 2 clusters Asked to drop 0 genes and 600 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [600] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: -0.032958984375 | max: 10.0859375 | % negative: 3.66666666666667 Only analysis elapsed time: 3.24131393432617 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: 3.34414315223694 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00603985786437988 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0375521183013916 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.933800935745239 Total calculations elapsed time: 4.32153606414795 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.36289000511169 Total elapsed time: 10.5379748344421 Checking uniformity for the cluster '01_0002' with 600 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0002, with size 600, is uniform Cluster 01_0002's shift to uniformity: -0.0203445505533575 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0366666666666667, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.37665544944664, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.0316666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42305229982216, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00333333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.43783135828069, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 2, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.50182972335853, isUniform = TRUE, clusterSize = 600 cluster 01_0002 is uniform Found 2 uniform and 0 non-uniform clusters Stopping: too few cells left to cluster Unclustered cell left: 0 The final raw clusterization contains [ 2 ] different clusters: 01_0001, 01_0002 Differential Expression Analysis - START * DEA on cluster '1' with 600 cells * DEA on cluster '2' with 600 cells Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Creating cells' uniform clustering: DONE findClustersMarkers - START Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' * Analysis of cluster: '3' * Analysis of cluster: '4' Log Fold Change Analysis - DONE findClustersMarkers - DONE findClustersMarkers - START Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' * Analysis of cluster: '3' * Analysis of cluster: '4' Log Fold Change Analysis - DONE findClustersMarkers - DONE findClustersMarkers - START Differential Expression Analysis - START * DEA on cluster '1' with 321 cells * DEA on cluster '2' with 295 cells * DEA on cluster '3' with 353 cells * DEA on cluster '4' with 231 cells Differential Expression Analysis - DONE Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' * Analysis of cluster: '3' * Analysis of cluster: '4' Log Fold Change Analysis - DONE findClustersMarkers - DONE [1] "Tested cluster: 1" Asked to drop 0 genes and 879 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [321] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: -0.0501708984375 | max: 14.515625 | % negative: 8.5 Only analysis elapsed time: 3.01551294326782 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: 3.01097393035889 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00596404075622559 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.02628493309021 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.947460889816284 Total calculations elapsed time: 3.99068379402161 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 4.92753100395203 Total elapsed time: 9.83713316917419 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: 2.79130792617798 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: 2.85820508003235 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00648403167724609 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0123710632324219 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.92808198928833 Total calculations elapsed time: 3.80514216423035 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 4.7107150554657 Total elapsed time: 9.29045295715332 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: 6.33450388908386 Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer counts Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Centering and scaling data matrix | | | 0% | |======================================================================| 100% PC_ 1 Positive: g-000558, g-000570, g-000499, g-000504, g-000546, g-000506, g-000503, g-000517, g-000596, g-000528 g-000527, g-000580, g-000592, g-000578, g-000509, g-000488, g-000555, g-000577, g-000534, g-000583 g-000598, g-000535, g-000512, g-000554, g-000519, g-000525, g-000548, g-000544, g-000502, g-000541 Negative: g-000133, g-000007, g-000074, g-000141, g-000057, g-000235, g-000170, g-000019, g-000195, g-000140 g-000183, g-000031, g-000046, g-000178, g-000177, g-000161, g-000157, g-000139, g-000011, g-000135 g-000125, g-000208, g-000061, g-000085, g-000204, g-000104, g-000237, g-000004, g-000038, g-000128 PC_ 2 Positive: g-000584, g-000583, g-000544, g-000519, g-000575, g-000516, g-000585, g-000486, g-000489, g-000539 g-000484, g-000502, g-000523, g-000595, g-000305, g-000574, g-000599, g-000589, g-000509, g-000538 g-000526, g-000551, g-000579, g-000590, g-000445, g-000556, g-000543, g-000501, g-000504, g-000570 Negative: g-000039, g-000050, g-000175, g-000078, g-000116, g-000189, g-000135, g-000047, g-000072, g-000087 g-000063, g-000235, g-000066, g-000109, g-000018, g-000074, g-000231, g-000136, g-000034, g-000207 g-000128, g-000167, g-000171, g-000049, g-000182, g-000013, g-000054, g-000062, g-000240, g-000158 PC_ 3 Positive: g-000015, g-000575, g-000483, g-000316, g-000025, g-000364, g-000050, g-000278, g-000443, g-000360 g-000332, g-000124, g-000212, g-000387, g-000536, g-000252, g-000251, g-000321, g-000501, g-000470 g-000582, g-000106, g-000455, g-000368, g-000081, g-000104, g-000437, g-000288, g-000386, g-000317 Negative: g-000211, g-000337, g-000129, g-000185, g-000397, g-000403, g-000253, g-000098, g-000390, g-000303 g-000052, g-000088, g-000463, g-000468, g-000236, g-000209, g-000005, g-000375, g-000342, g-000262 g-000388, g-000091, g-000413, g-000285, g-000003, g-000095, g-000142, g-000205, g-000432, g-000241 PC_ 4 Positive: g-000334, g-000398, g-000292, g-000095, g-000097, g-000202, g-000382, g-000195, g-000007, g-000079 g-000086, g-000240, g-000263, g-000317, g-000576, g-000557, g-000160, g-000154, g-000214, g-000228 g-000313, g-000053, g-000524, g-000374, g-000568, g-000188, g-000358, g-000528, g-000362, g-000150 Negative: g-000379, g-000193, g-000212, g-000434, g-000593, g-000513, g-000177, g-000223, g-000069, g-000131 g-000162, g-000345, g-000462, g-000484, g-000448, g-000229, g-000365, g-000302, g-000010, g-000366 g-000051, g-000535, g-000269, g-000270, g-000155, g-000529, g-000373, g-000008, g-000393, g-000306 PC_ 5 Positive: g-000518, g-000108, g-000186, g-000170, g-000401, g-000337, g-000047, g-000599, g-000432, g-000578 g-000042, g-000065, g-000493, g-000261, g-000533, g-000256, g-000560, g-000596, g-000368, g-000381 g-000535, g-000338, g-000215, g-000159, g-000365, g-000234, g-000173, g-000387, g-000225, g-000272 Negative: g-000451, g-000339, g-000295, g-000328, g-000544, g-000061, g-000227, g-000391, g-000556, g-000237 g-000067, g-000165, g-000449, g-000591, g-000087, g-000129, g-000197, g-000203, g-000487, g-000505 g-000333, g-000029, g-000271, g-000064, g-000583, g-000156, g-000448, g-000153, g-000526, g-000393 Computing nearest neighbor graph Computing SNN Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 1200 Number of edges: 55940 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.5920 Number of communities: 4 Elapsed time: 0 seconds Clusterizations found: RNA_snn_res.0.8, seurat_clusters Conditions found: orig.ident Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Cotan genes' COEX estimation not requested Total elapsed time: 6.56837296485901 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: 3.58388614654541 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: 3.60298895835876 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00715804100036621 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0470991134643555 Estimating genes' COEX Calculate genes' COEX elapsed time: 1.00641298294067 Total calculations elapsed time: 4.66365909576416 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.62451982498169 Total elapsed time: 11.1739609241486 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: 6.34999895095825 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: 3.08612108230591 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: 3.15145182609558 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00712108612060547 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0378119945526123 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.944968938827515 Total calculations elapsed time: 4.14135384559631 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.08953309059143 Total elapsed time: 10.1395139694214 Checking uniformity for the cluster '1_2-merge' with 574 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 1_2-merge, with size 574, is not uniform Cluster 1_2-merge's shift to uniformity: 0.0820221369127518 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.326666666666667, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.37902213691275, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.28, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.41724738266283, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.0333333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.42971854140312, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 20, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.5067755752749, isUniform = FALSE, clusterSize = 574 Clusters 1 and 2 cannot be merged *3_4-merge Asked to drop 0 genes and 574 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [626] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: -0.03839111328125 | max: 17.40625 | % negative: 6.66666666666667 Only analysis elapsed time: 3.13874912261963 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: 3.16988396644592 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00699615478515625 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0355179309844971 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.974602937698364 Total calculations elapsed time: 4.18700098991394 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.09707593917847 Total elapsed time: 10.1548111438751 Checking uniformity for the cluster '3_4-merge' with 626 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 3_4-merge, with size 626, is not uniform Cluster 3_4-merge's shift to uniformity: 0.0914611744346074 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.248333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.38846117443461, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.218333333333333, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42066795244751, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.0366666666666667, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.45442688129939, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 22, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.52592182249635, isUniform = FALSE, clusterSize = 626 Clusters 3 and 4 cannot be merged Finished the first batch - no merges were executed Start merging nearest clusters: iteration 2 Differential Expression Analysis - START * DEA on cluster '1' with 353 cells * DEA on cluster '2' with 221 cells * DEA on cluster '3' with 315 cells * DEA on cluster '4' with 311 cells Differential Expression Analysis - DONE Updating check results for the 2 already tested pairs to align to new checker 2 new clusters pairs to be tested for merging: c("2", "3") c("2", "4") *2_3-merge Asked to drop 0 genes and 664 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [536] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: -0.0390625 | max: 12.59375 | % negative: 9.16666666666667 Only analysis elapsed time: 3.07696890830994 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: 3.00164699554443 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00791692733764648 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0212249755859375 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.929602146148682 Total calculations elapsed time: 3.9603910446167 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 4.9336268901825 Total elapsed time: 9.82811784744263 Checking uniformity for the cluster '2_3-merge' with 536 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 2_3-merge, with size 536, is not uniform Cluster 2_3-merge's shift to uniformity: 0.102213698003777 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.29, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.39921369800378, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.251666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.45276697088286, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.05, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.49016449535422, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 30, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.54477108741147, isUniform = FALSE, clusterSize = 536 Clusters 2 and 3 cannot be merged *2_4-merge Asked to drop 0 genes and 668 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [532] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: -0.04754638671875 | max: 10.234375 | % negative: 5 Only analysis elapsed time: 2.98316216468811 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: 3.12237191200256 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00612807273864746 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.032153844833374 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.932757139205933 Total calculations elapsed time: 4.09341096878052 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.07063579559326 Total elapsed time: 9.9207808971405 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: 3.06539678573608 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: 3.14718580245972 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00623011589050293 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0374341011047363 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.956816911697388 Total calculations elapsed time: 4.14766693115234 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.11972618103027 Total elapsed time: 10.0608541965485 Checking uniformity for the cluster '1_3-merge' with 668 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 1_3-merge, with size 668, is not uniform Cluster 1_3-merge's shift to uniformity: 0.177923707405303 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.33, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.5749237074053, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.31, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.6368755707341, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.128333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.65704996173771, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 77, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.68881338289977, isUniform = FALSE, clusterSize = 668 Clusters 1 and 3 cannot be merged *1_4-merge Asked to drop 0 genes and 536 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [664] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: -0.0164794921875 | max: 5.5595703125 | % negative: 0.166666666666667 Only analysis elapsed time: 3.1065239906311 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: 3.14370799064636 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00759506225585938 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0409979820251465 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.995582103729248 Total calculations elapsed time: 4.18788313865662 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.16099095344543 Total elapsed time: 10.119668006897 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 = 1.53527735568616, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.316666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.55951216335001, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.0983333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.59105696847609, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 59, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.64605433203111, isUniform = FALSE, clusterSize = 664 Clusters 1 and 4 cannot be merged Clusters 2 and 1 will be merged Clusters 3 and 4 will be merged Executed 2 merges Start merging nearest clusters: iteration 4 Differential Expression Analysis - START * DEA on cluster '1_2-merge' with 574 cells * DEA on cluster '3_4-merge' with 626 cells Differential Expression Analysis - DONE Updating check results for the 6 already tested pairs to align to new checker 1 new clusters pairs to be tested for merging: c("1_2-merge", "3_4-merge") *1_2-merge_3_4-merge-merge Asked to drop no genes or cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Only analysis elapsed time: 3.48954391479492 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: 3.50655698776245 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00649619102478027 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.042503833770752 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.981557130813599 Total calculations elapsed time: 4.53711414337158 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.50092506408691 Total elapsed time: 10.8705070018768 Checking uniformity for the cluster '1_2-merge_3_4-merge-merge' with 1200 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 1_2-merge_3_4-merge-merge, with size 1200, is not uniform Cluster 1_2-merge_3_4-merge-merge's shift to uniformity: 0.173174985379327 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.415, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.57017498537933, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.388333333333333, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.61240081401504, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.15, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.64046660675367, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 90, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.66512085964758, isUniform = FALSE, clusterSize = 1200 Clusters 1_2-merge and 3_4-merge cannot be merged No clusters will be merged None of the remaining tested cluster pairs could be merged Executed all merges for threshold 1.397 out of 7 checks The final merged clusterization contains [2] different clusters: 1_2-merge, 3_4-merge Differential Expression Analysis - START * DEA on cluster '1' with 574 cells * DEA on cluster '2' with 626 cells Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Merging cells' uniform clustering: DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' Log Fold Change Analysis - DONE Asked to drop 0 genes and 626 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [574] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: -0.0340576171875 | max: 10.4375 | % negative: 4.33333333333333 Only analysis elapsed time: 3.17232203483582 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: 3.15644001960754 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00677895545959473 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.034459114074707 Estimating genes' COEX Calculate genes' COEX elapsed time: 0.912153005599976 Total calculations elapsed time: 4.10983109474182 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.02688407897949 Total elapsed time: 10.0841951370239 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: 3.05730795860291 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: 3.24962592124939 Calculating genes' COEX normalization factor Calculate genes' normalization factor elapsed time: 0.00705099105834961 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0330500602722168 Estimating genes' COEX Calculate genes' COEX elapsed time: 1.08319997787476 Total calculations elapsed time: 4.37292695045471 Calculate genes' COEX (legacy): DONE Only genes' COEX elapsed time: 5.37074112892151 Total elapsed time: 10.3357510566711 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 1 | SKIP 0 | PASS 572 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 572 ] > > proc.time() user system elapsed 806.673 10.914 824.496
COTAN.Rcheck/COTAN-Ex.timings
name | user | system | elapsed | |
COTAN_Legacy | 0.003 | 0.001 | 0.003 | |
COTAN_ObjectCreation | 12.158 | 0.326 | 12.571 | |
CalculatingCOEX | 58.306 | 1.154 | 59.707 | |
ClustersList | 0.008 | 0.002 | 0.010 | |
Conversions | 6.270 | 0.136 | 6.447 | |
GenesStatistics | 12.280 | 0.388 | 12.532 | |
HandleMetaData | 0.093 | 0.008 | 0.103 | |
HandlingClusterizations | 42.845 | 1.226 | 43.684 | |
HandlingConditions | 0.133 | 0.008 | 0.143 | |
HeatmapPlots | 35.686 | 0.938 | 36.852 | |
LoggingFunctions | 0.002 | 0.002 | 0.004 | |
ParametersEstimations | 25.977 | 0.791 | 26.882 | |
RawDataCleaning | 4.823 | 0.300 | 4.944 | |
RawDataGetters | 0.082 | 0.006 | 0.089 | |
UniformClusters | 206.733 | 3.124 | 209.496 | |
getColorsVector | 0.002 | 0.015 | 0.001 | |