Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-25 17:43 -0400 (Tue, 25 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 449/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
COTAN 2.4.3 (landing page) Galfrè Silvia Giulia
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 2.4.3 |
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_2.4.3.tar.gz |
StartedAt: 2024-06-24 15:51:35 -0400 (Mon, 24 Jun 2024) |
EndedAt: 2024-06-24 16:16:23 -0400 (Mon, 24 Jun 2024) |
EllapsedTime: 1487.9 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_2.4.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/COTAN.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘COTAN/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘COTAN’ version ‘2.4.3’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘COTAN’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE 'library' or 'require' call to ‘torch’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Unexported object imported by a ':::' call: ‘ggplot2:::ggname’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE GDIPlot: no visible binding for global variable ‘sum.raw.norm’ GDIPlot: no visible binding for global variable ‘GDI’ UMAPPlot: no visible binding for global variable ‘x’ UMAPPlot: no visible binding for global variable ‘y’ calculateCoex_Legacy: no visible binding for global variable ‘expectedNN’ calculateCoex_Legacy: no visible binding for global variable ‘expectedNY’ calculateCoex_Legacy: no visible binding for global variable ‘expectedYN’ calculateCoex_Legacy: no visible binding for global variable ‘expectedYY’ calculateCoex_Legacy: no visible binding for global variable ‘observedYY’ calculateCoex_Legacy: no visible binding for global variable ‘.’ calculateG: no visible binding for global variable ‘observedNN’ calculateG: no visible binding for global variable ‘observedNY’ calculateG: no visible binding for global variable ‘observedYN’ calculateG: no visible binding for global variable ‘observedYY’ calculateG: no visible binding for global variable ‘expectedNN’ calculateG: no visible binding for global variable ‘expectedNY’ calculateG: no visible binding for global variable ‘expectedYN’ calculateG: no visible binding for global variable ‘expectedYY’ calculatePartialCoex: no visible binding for global variable ‘expectedNN’ calculatePartialCoex: no visible binding for global variable ‘expectedNY’ calculatePartialCoex: no visible binding for global variable ‘expectedYN’ calculatePartialCoex: no visible binding for global variable ‘expectedYY’ calculatePartialCoex: no visible binding for global variable ‘observedYY’ calculatePartialCoex: no visible binding for global variable ‘.’ cellsUniformClustering: no visible binding for global variable ‘objSeurat’ cellsUniformClustering: no visible binding for global variable ‘usedMaxResolution’ cellsUniformClustering: no visible binding for global variable ‘permMap’ checkClusterUniformity: ... may be used in an incorrect context: ‘c(..., nuPlot, zoomedNuPlot)’ checkClusterUniformity: no visible binding for global variable ‘nuPlot’ checkClusterUniformity: no visible binding for global variable ‘zoomedNuPlot’ cleanPlots: no visible binding for global variable ‘PC1’ cleanPlots: no visible binding for global variable ‘PC2’ cleanPlots: no visible binding for global variable ‘n’ cleanPlots: no visible binding for global variable ‘means’ cleanPlots: no visible binding for global variable ‘nu’ clustersMarkersHeatmapPlot: no visible binding for global variable ‘condName’ clustersMarkersHeatmapPlot: no visible binding for global variable ‘conditions’ clustersSummaryPlot: no visible binding for global variable ‘keys’ clustersSummaryPlot: no visible binding for global variable ‘values’ clustersSummaryPlot: no visible binding for global variable ‘CellNumber’ clustersSummaryPlot: no visible binding for global variable ‘ExpGenes’ clustersSummaryPlot: no visible binding for global variable ‘Cluster’ clustersSummaryPlot: no visible binding for global variable ‘Condition’ establishGenesClusters: no visible binding for global variable ‘secondaryMarkers’ establishGenesClusters: no visible binding for global variable ‘GCS’ establishGenesClusters: no visible binding for global variable ‘rankGenes’ expectedContingencyTables: no visible binding for global variable ‘expectedN’ expectedPartialContingencyTables: no visible binding for global variable ‘expectedNN’ expectedPartialContingencyTables: no visible binding for global variable ‘expectedN’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘group’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘y’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘x’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘width’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘violinwidth’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘xmax’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘xminv’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘xmaxv’ heatmapPlot: no visible binding for global variable ‘g2’ mergeUniformCellsClusters : testPairListMerge: no visible binding for global variable ‘cl1’ mergeUniformCellsClusters : testPairListMerge: no visible binding for global variable ‘cl2’ mergeUniformCellsClusters: no visible binding for global variable ‘permMap’ mitochondrialPercentagePlot: no visible binding for global variable ‘mit.percentage’ observedContingencyTables: no visible binding for global variable ‘observedY’ observedPartialContingencyTables: no visible binding for global variable ‘observedYY’ observedPartialContingencyTables: no visible binding for global variable ‘observedY’ scatterPlot: no visible binding for global variable ‘.x’ calculateCoex,COTAN: no visible binding for global variable ‘useTorch’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘rawNorm’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘nu’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘lambda’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘a’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘hk’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘clusters’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘clusterData’ Undefined global functions or variables: . .x CellNumber Cluster Condition ExpGenes GCS GDI PC1 PC2 a cl1 cl2 clusterData clusters condName conditions expectedN expectedNN expectedNY expectedYN expectedYY g2 group hk keys lambda means mit.percentage n nu nuPlot objSeurat observedNN observedNY observedY observedYN observedYY permMap rankGenes rawNorm secondaryMarkers sum.raw.norm useTorch usedMaxResolution values violinwidth width x xmax xmaxv xminv y zoomedNuPlot * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed UniformClusters 197.094 1.993 199.991 CalculatingCOEX 73.143 1.334 76.117 HeatmapPlots 56.363 1.647 58.424 ParametersEstimations 31.441 1.013 32.765 HandlingClusterizations 24.911 0.539 26.452 GenesStatistics 14.108 0.249 14.571 COTANObjectCreation 12.525 0.274 12.999 RawDataCleaning 9.212 0.167 9.387 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘outputTestDatasetCreation.R’ Running ‘spelling.R’ Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/COTAN.Rcheck/00check.log’ for details.
COTAN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL COTAN ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘COTAN’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Note: ... may be used in an incorrect context ** 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 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > > # Creates the files to be reloaded by the tests for comparisons > library(zeallot) > > outputTestDatasetCreation <- function(testsDir = file.path("tests", + "testthat")) { + utils::data("test.dataset", package = "COTAN") + options(parallelly.fork.enable = TRUE) + + obj <- COTAN(raw = test.dataset) + obj <- initializeMetaDataset(obj, GEO = " ", + sequencingMethod = "artificial", + sampleCondition = "test") + + obj <- proceedToCoex(obj, cores = 6L, saveObj = FALSE) + #saveRDS(obj, file = file.path(testsDir,"temp.RDS")) + + cells.names.test <- getCells(obj)[c(1L:10L, 591L:610L, 991L:1000L)] + genes.names.test <- getGenes(obj)[c(1L:10L, 291L:310L, 591L: 600L)] + saveRDS(cells.names.test, file.path(testsDir, "cells.names.test.RDS")) + saveRDS(genes.names.test, file.path(testsDir, "genes.names.test.RDS")) + + dispersion.test <- getDispersion(obj)[genes.names.test] + saveRDS(dispersion.test, file.path(testsDir, "dispersion.test.RDS")) + + raw.norm.test <- getNormalizedData(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), method = "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 0.250 0.069 0.313
COTAN.Rcheck/tests/spelling.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > if (requireNamespace('spelling', quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) NULL > > proc.time() user system elapsed 0.230 0.070 0.287
COTAN.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > Sys.setenv(R_TESTS = "") > library(testthat) > library(COTAN) > test_check("COTAN") Setting new log level to 4 Initializing `COTAN` meta-data Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.9033203125 | max: 4.6796875 | % negative: 10 Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.95324182510376 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0013279914855957 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0071871280670166 Estimating genes' coex Calculate genes' coex elapsed time: 0.901365995407104 Total calculations elapsed time: 3.86312294006348 Calculate genes' coex (legacy): DONE Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate dispersion: START Effective number of cores used: 1 Executing 4 genes batches from [1:2] to [7:8] Executing 1 genes batches from [9:10] to [9:10] Estimate dispersion: DONE dispersion | min: 0.9033203125 | max: 4.6796875 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 4 cells batches from [1:3] to [10:11] Executing 3 cells batches from [12:14] to [18:20] Estimate nu: DONE nu change (abs) | max: 1.75595238095238 | median: 1.07174634176587 | mean: 1.07174634176587 Estimate 'dispersion'/'nu': START Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 1.0362548828125 | max: 4.60986328125 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.0265938895089288 | median: 0.0144680038331048 | mean: 0.0144680038331048 Nu mean: 1.69633192486233 Marginal errors | max: 1.95570586131367 | median 1.32068160171502 | mean: 1.33375826507259 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.058837890625 | max: 3.528076171875 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.416683423613994 | median: 0.239880630367975 | mean: 0.239880630367975 Nu mean: 0.823197206753982 Marginal errors | max: 0.836359531101206 | median 0.703684202571891 | mean: 0.645537958989614 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.32879638671875 | max: 4.0302734375 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.164237872898673 | median: 0.0955985184389135 | mean: 0.0955985184389135 Nu mean: 1.06863935445976 Marginal errors | max: 0.259872988828242 | median 0.213703042752633 | mean: 0.197386407582083 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.2294921875 | max: 3.8720703125 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.055185575120883 | median: 0.0319991762044448 | mean: 0.0319991762044448 Nu mean: 0.976813601083562 Marginal errors | max: 0.0951586919577032 | median 0.079429703709466 | mean: 0.0724140148396648 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.2637939453125 | max: 3.929443359375 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.0196211148938294 | median: 0.01138609597457 | mean: 0.01138609597457 Nu mean: 1.00823501891926 Marginal errors | max: 0.0327747321002292 | median 0.0272104747849538 | mean: 0.0248963830312038 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.25177001953125 | max: 3.90966796875 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.00670099066960717 | median: 0.00388888266671264 | mean: 0.00388888266671264 Nu mean: 0.997187891997105 Marginal errors | max: 0.0114324509186883 | median 0.0094232649770607 | mean: 0.00863113610779571 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.25592041015625 | max: 3.91650390625 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.00230093811689414 | median: 0.00132529122122246 | mean: 0.00132529122122246 Nu mean: 1.00097564689567 Marginal errors | max: 0.00387133150664631 | median 0.0031091017608853 | mean: 0.00286071175800213 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.2545166015625 | max: 3.914306640625 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.000837011646904529 | median: 0.000470837393363011 | mean: 0.000470837393363011 Nu mean: 0.999633825746458 Marginal errors | max: 0.00122501723202006 | median 0.00102126435760308 | mean: 0.000943992659051318 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.2550048828125 | max: 3.9150390625 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.000209227351122054 | median: 0.000122070312500028 | mean: 0.000122070312500028 Nu mean: 1.00008715703862 Marginal errors | max: 0.000364602956581805 | median 0.000313956936819793 | mean: 0.000282899574318485 Estimate dispersion/nu: DONE Estimate 'dispersion'/'nu': START Initializing `COTAN` meta-data Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.9033203125 | max: 4.6796875 | % negative: 10 While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.17107105255127 Calculating genes' coex normalization factor Fraction of genes' with very low expected contingency tables: 0.181818181818182 Calculate genes' normalization factor elapsed time: 0.000878095626831055 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00412988662719727 Estimating genes' coex Calculate genes' coex elapsed time: 1.09739303588867 Total calculations elapsed time: 4.27347207069397 Calculate genes' coex (legacy): DONE Calculate cells' coex (legacy): START Retrieving expected cells' contingency table calculating NN.. done calculating YN..NY..YY..t().. done Expected cells' contingency table elapsed time: 3.12460088729858 Calculating cells' coex normalization factor Fraction of cells' with very low expected contingency tables: 0 Calculate cells' normalization factor elapsed time: 0.000832080841064453 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.0027320384979248 Estimating cells' coex Calculate cells' coex elapsed time: 1.09541988372803 Total calculations elapsed time: 4.2235848903656 Calculate cells' coex (legacy): DONE Initializing `COTAN` meta-data Initializing `COTAN` meta-data Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate 'dispersion'/'nu': START Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.903564453125 | max: 4.679443359375 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014 Nu mean: 1.68489292689732 Marginal errors | max: 1.73564890252257 | median 1.37996360874076 | mean: 1.32180348113228 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.0655517578125 | max: 3.5439453125 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.402649984216273 | median: 0.231868788425666 | mean: 0.231868788425666 Nu mean: 0.829218804209393 Marginal errors | max: 0.80321315986594 | median 0.677497553540581 | mean: 0.61937543089282 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.3260498046875 | max: 4.026123046875 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.158004893526231 | median: 0.0919692884670312 | mean: 0.0919692884670312 Nu mean: 1.0660356050592 Marginal errors | max: 0.250724014302326 | median 0.206232152124436 | mean: 0.190425623677198 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.23040771484375 | max: 3.8736572265625 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.0532774732102337 | median: 0.0308837890624999 | mean: 0.0308837890624999 Nu mean: 0.977606315852266 Marginal errors | max: 0.0916983669060123 | median 0.0765266929824948 | mean: 0.0697593208689684 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.26348876953125 | max: 3.928955078125 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.0189966206463044 | median: 0.0110199320575908 | mean: 0.0110199320575908 Nu mean: 1.00797668858871 Marginal errors | max: 0.0317151207459254 | median 0.026270214227825 | mean: 0.0240886952086962 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.2518310546875 | max: 3.9097900390625 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.00670088501353994 | median: 0.00388888101583662 | mean: 0.00388888101583662 Nu mean: 0.997187996002297 Marginal errors | max: 0.0113693316356223 | median 0.00939669372836249 | mean: 0.00860715734056932 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.2559814453125 | max: 3.9166259765625 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.00251007446998996 | median: 0.00144735987374958 | mean: 0.00144735987374958 Nu mean: 1.00106271459624 Marginal errors | max: 0.00406746973787442 | median 0.00343393462175534 | mean: 0.00313496757119527 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.25445556640625 | max: 3.9140625 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.000837027590858019 | median: 0.000488281249999889 | mean: 0.000488281249999889 Nu mean: 0.999651253659142 Marginal errors | max: 0.00143433714371533 | median 0.00116636244706747 | mean: 0.00109289166947839 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.2550048828125 | max: 3.9150390625 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.000209227688885871 | median: 0.0001220703125 | mean: 0.0001220703125 Nu mean: 1.00008715737639 Marginal errors | max: 0.000379524846207957 | median 0.000325685250686547 | mean: 0.000295532844332236 Estimate dispersion/nu: DONE While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.21242809295654 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.000663042068481445 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00162696838378906 Estimating genes' coex Calculate genes' coex elapsed time: 1.07012701034546 Total calculations elapsed time: 4.28484511375427 Calculate genes' coex (legacy): DONE Calculate cells' coex (legacy): START Retrieving expected cells' contingency table calculating NN.. done calculating YN..NY..YY..t().. done Expected cells' contingency table elapsed time: 3.12498998641968 Calculating cells' coex normalization factor Calculate cells' normalization factor elapsed time: 0.000695943832397461 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00164794921875 Estimating cells' coex Calculate cells' coex elapsed time: 1.0502200126648 Total calculations elapsed time: 4.17755389213562 Calculate cells' 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: 0.325 Retrieving observed genes' yes/yes partial contingency table calculating partial YY.. done Estimating genes' partial coex Calculate genes' partial coex: DONE Calculate cells' partial coex: START Retrieving expected cells' partial contingency table calculating partial NN.. done calculating partial YN..NY..YY.. done Calculating cells' partial coex normalization factor Fraction of genes with very low expected contingency tables: 0 Retrieving observed cells' yes/yes partial contingency table calculating partial YY.. done Estimating cells' partial coex Calculate cells' partial coex: DONE Asked to drop 2 genes and 0 cells Asked to drop 0 genes and 4 cells Asked to drop 2 genes and 2 cells Attaching package: 'rlang' The following objects are masked from 'package:testthat': is_false, is_null, is_true Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells calculating YY.. done calculating YY.. done calculating YN..NY..NN..t().. done Estimate dispersion: START Effective number of cores used: 1 Executing 3 genes batches from [1:3] to [8:10] Estimate dispersion: DONE dispersion | min: 0.9033203125 | max: 4.6796875 | % negative: 10 calculating NN.. done calculating NN.. done calculating NY..YN..YY..t().. done Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.17617702484131 Calculating genes' coex normalization factor Fraction of genes' with very low expected contingency tables: 0.181818181818182 Calculate genes' normalization factor elapsed time: 0.000890016555786133 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0017240047454834 Estimating genes' coex Calculate genes' coex elapsed time: 1.0972797870636 Total calculations elapsed time: 4.27607083320618 Calculate genes' coex (legacy): DONE While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.2501540184021 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.000879049301147461 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00243186950683594 Estimating genes' coex Calculate genes' coex elapsed time: 1.01369690895081 Total calculations elapsed time: 4.26716184616089 Calculate genes' coex (legacy): DONE Calculate genes' partial coex: START Retrieving expected genes' partial contingency table calculating partial NN.. done calculating partial NY..YN..YY.. done Calculating genes' partial coex normalization factor Fraction of genes with very low expected contingency tables: 0.1 Retrieving observed genes' yes/yes partial contingency table calculating partial YY.. done Estimating genes' partial coex Calculate genes' partial coex: DONE Calculate genes' partial coex: START Retrieving expected genes' partial contingency table calculating partial NN.. done calculating partial NY..YN..YY.. done Calculating genes' partial coex normalization factor Fraction of genes with very low expected contingency tables: 0.4 Retrieving observed genes' yes/yes partial contingency table calculating partial YY.. done Estimating genes' partial coex Calculate genes' partial coex: DONE Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells calculating YY.. done calculating YY.. done calculating NY..YN..NN..t().. done Estimate 'dispersion'/'nu': START Estimate dispersion: START Effective number of cores used: 1 Executing 3 genes batches from [1:3] to [8:10] Estimate dispersion: DONE dispersion | min: 0.903564453125 | max: 4.679443359375 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 4 cells batches from [1:4] to [13:16] Executing 1 cells batches from [17:20] to [17:20] Estimate nu: DONE nu change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014 Nu mean: 1.68489292689732 Marginal errors | max: 0.25535328937316 | median 0.0807577993228135 | mean: 0.101980750205762 Estimate dispersion: START Effective number of cores used: 1 Executing 3 genes batches from [1:3] to [8:10] Estimate dispersion: DONE dispersion | min: 1.037109375 | max: 4.6107177734375 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 4 cells batches from [1:4] to [13:16] Executing 1 cells batches from [17:20] to [17:20] Estimate nu: DONE nu change (abs) | max: 0.0273438105507502 | median: 0.0148852611818011 | mean: 0.0148852611818011 Nu mean: 1.69735147626627 Marginal errors | max: 0.00326864580272002 | median 0.00111524657842743 | mean: 0.00131556083122533 Estimate dispersion: START Effective number of cores used: 1 Executing 3 genes batches from [1:3] to [8:10] Estimate dispersion: DONE dispersion | min: 1.03887939453125 | max: 4.6097412109375 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 4 cells batches from [1:4] to [13:16] Executing 1 cells batches from [17:20] to [17:20] Estimate nu: DONE nu change (abs) | max: 0 | median: 0 | mean: 0 Nu mean: 1.69735147626627 Marginal errors | max: 7.56328383637594e-05 | median 1.72948087246994e-05 | mean: 2.99252342145451e-05 Estimate dispersion/nu: DONE calculating NN.. done calculating NN.. done calculating YN..NY..YY..t().. done Calculate cells' coex (legacy): START Retrieving expected cells' contingency table calculating NN.. done calculating YN..NY..YY..t().. done Expected cells' contingency table elapsed time: 3.22014403343201 Calculating cells' coex normalization factor Fraction of cells' with very low expected contingency tables: 0 Calculate cells' normalization factor elapsed time: 0.00081181526184082 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00156903266906738 Estimating cells' coex Calculate cells' coex elapsed time: 1.09532403945923 Total calculations elapsed time: 4.31784892082214 Calculate cells' coex (legacy): DONE Calculate cells' partial coex: START Retrieving expected cells' partial contingency table calculating partial NN.. done calculating partial YN..NY..YY.. done Calculating cells' partial coex normalization factor Fraction of genes with very low expected contingency tables: 0 Retrieving observed cells' yes/yes partial contingency table calculating partial YY.. done Estimating cells' partial coex Calculate cells' partial coex: DONE Calculate cells' partial coex: START Retrieving expected cells' partial contingency table calculating partial NN.. done calculating partial YN..NY..YY.. done Calculating cells' partial coex normalization factor Fraction of genes with very low expected contingency tables: 0 Retrieving observed cells' yes/yes partial contingency table calculating partial YY.. done Estimating cells' partial coex Calculate cells' partial coex: DONE Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate 'dispersion'/'nu': START Estimate dispersion: START Effective number of cores used: 1 Executing 3 genes batches from [1:3] to [8:10] Estimate dispersion: DONE dispersion | min: 0.903564453125 | max: 4.679443359375 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 4 cells batches from [1:4] to [13:16] Executing 1 cells batches from [17:20] to [17:20] Estimate nu: DONE nu change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014 Nu mean: 1.68489292689732 Marginal errors | max: 0.25535328937316 | median 0.0807577993228135 | mean: 0.101980750205762 Estimate dispersion: START Effective number of cores used: 1 Executing 3 genes batches from [1:3] to [8:10] Estimate dispersion: DONE dispersion | min: 1.037109375 | max: 4.6107177734375 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 4 cells batches from [1:4] to [13:16] Executing 1 cells batches from [17:20] to [17:20] Estimate nu: DONE nu change (abs) | max: 0.0273438105507502 | median: 0.0148852611818011 | mean: 0.0148852611818011 Nu mean: 1.69735147626627 Marginal errors | max: 0.00326864580272002 | median 0.00111524657842743 | mean: 0.00131556083122533 Estimate dispersion: START Effective number of cores used: 1 Executing 3 genes batches from [1:3] to [8:10] Estimate dispersion: DONE dispersion | min: 1.03887939453125 | max: 4.6097412109375 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 4 cells batches from [1:4] to [13:16] Executing 1 cells batches from [17:20] to [17:20] Estimate nu: DONE nu change (abs) | max: 0 | median: 0 | mean: 0 Nu mean: 1.69735147626627 Marginal errors | max: 7.56328383637594e-05 | median 1.72948087246994e-05 | mean: 2.99252342145451e-05 Estimate dispersion/nu: DONE Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.30710601806641 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.000777959823608398 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00176715850830078 Estimating genes' coex Calculate genes' coex elapsed time: 1.10756587982178 Total calculations elapsed time: 4.41721701622009 Calculate genes' coex (legacy): DONE Calculating S: START Calculating S: DONE Calculating G: START calculating YY.. done calculating YN..NY..NN..t().. done calculating NN.. done calculating NY..YN..YY..t().. done Estimating G Calculating G: DONE Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values genome wide on columns and genome wide on rows calculating PValues: DONE Using G Calculating G: START calculating YY.. done calculating YN..NY..NN..t().. done calculating NN.. done calculating NY..YN..YY..t().. done Estimating G Calculating G: DONE calculating PValues: START Get p-values on a set of genes on columns and on a set of genes on rows calculating PValues: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE Calculate GDI dataframe: START Using G Calculating G: START calculating YY.. done calculating YN..NY..NN..t().. done calculating NN.. done calculating NY..YN..YY..t().. done Estimating G Calculating G: DONE S matrix sorted Calculate GDI dataframe: DONE Calculating S: START Calculating S: DONE S matrix sorted S matrix sorted Initializing `COTAN` meta-data Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Only analysis elapsed time: 3.98124694824219 Cotan genes' coex estimation started Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 4.70883202552795 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00978398323059082 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0684380531311035 Estimating genes' coex Calculate genes' coex elapsed time: 1.08494210243225 Total calculations elapsed time: 5.8719961643219 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.94370698928833 Total elapsed time: 11.934602022171 Initializing `COTAN` meta-data Condition test n cells 1200 Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Only analysis elapsed time: 3.95807600021362 Cotan genes' coex estimation started Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 4.61939096450806 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0091559886932373 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0740311145782471 Estimating genes' coex Calculate genes' coex elapsed time: 1.06034088134766 Total calculations elapsed time: 5.7629189491272 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.76142692565918 Total elapsed time: 11.7319009304047 Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and genome wide on rows calculating PValues: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE Initializing `COTAN` meta-data Condition test n cells 1200 Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Only analysis elapsed time: 3.92467999458313 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 4.74821400642395 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00861310958862305 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0673258304595947 Estimating genes' coex Calculate genes' coex elapsed time: 1.100426197052 Total calculations elapsed time: 5.92457914352417 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 7.04353880882263 Total elapsed time: 12.0319199562073 Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and genome wide on rows calculating PValues: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE Initializing `COTAN` meta-data Condition test n cells 1200 Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Only analysis elapsed time: 3.89041090011597 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 4.67078995704651 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00857806205749512 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0716791152954102 Estimating genes' coex Calculate genes' coex elapsed time: 1.09266495704651 Total calculations elapsed time: 5.84371209144592 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.92267799377441 Total elapsed time: 11.9199409484863 Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and genome wide on rows calculating PValues: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE Initializing `COTAN` meta-data Asked to drop 0 genes and 1160 cells Cotan analysis functions started Asked to drop 31 genes and 0 cells Genes/cells selection done: dropped [31] genes and [0] cells Working on [569] genes and [40] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:569] to [1:569] Estimate dispersion: DONE dispersion | min: -0.2119140625 | max: 85.5 | % negative: 62.2144112478032 Cotan genes' coex estimation not requested Total elapsed time: 5.30836606025696 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: 3.27263689041138 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00897312164306641 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0088958740234375 Estimating genes' coex Calculate genes' coex elapsed time: 0.981590032577515 Total calculations elapsed time: 4.2720959186554 Calculate genes' coex (legacy): DONE While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.27980995178223 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00839996337890625 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0086820125579834 Estimating genes' coex Calculate genes' coex elapsed time: 1.09307599067688 Total calculations elapsed time: 4.389967918396 Calculate genes' coex (legacy): DONE While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.20361518859863 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00697088241577148 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00780200958251953 Estimating genes' coex Calculate genes' coex elapsed time: 1.07651209831238 Total calculations elapsed time: 4.2949001789093 Calculate genes' coex (legacy): 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 PCA: START PCA: DONE Hierarchical clustering: START Hierarchical clustering: DONE Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Cotan genes' coex estimation not requested Total elapsed time: 10.6781339645386 Saving elaborated data locally at: /tmp/RtmpXSwR8K/test.cotan.RDS Creating cells' uniform clustering: START In iteration 1 the number of cells to re-cluster is 1200 cells belonging to 0 clusters Creating Seurat object: START Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer counts Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Centering and scaling data matrix | | | 0% | |======================================================================| 100% PC_ 1 Positive: g-000558, g-000570, g-000499, g-000504, g-000546, g-000506, g-000503, g-000517, g-000596, g-000528 g-000527, g-000580, g-000592, g-000578, g-000509, g-000488, g-000555, g-000577, g-000534, g-000583 g-000598, g-000535, g-000512, g-000554, g-000519, g-000525, g-000548, g-000544, g-000502, g-000541 Negative: g-000133, g-000007, g-000074, g-000141, g-000057, g-000235, g-000170, g-000019, g-000195, g-000140 g-000183, g-000031, g-000046, g-000178, g-000177, g-000161, g-000157, g-000139, g-000011, g-000135 g-000125, g-000208, g-000061, g-000085, g-000204, g-000104, g-000237, g-000004, g-000038, g-000128 PC_ 2 Positive: g-000039, g-000050, g-000175, g-000078, g-000116, g-000189, g-000135, g-000047, g-000072, g-000087 g-000063, g-000235, g-000066, g-000109, g-000018, g-000074, g-000231, g-000136, g-000034, g-000207 g-000128, g-000167, g-000171, g-000049, g-000182, g-000013, g-000054, g-000062, g-000240, g-000158 Negative: g-000584, g-000583, g-000544, g-000519, g-000575, g-000516, g-000585, g-000486, g-000489, g-000539 g-000484, g-000502, g-000523, g-000595, g-000305, g-000574, g-000599, g-000589, g-000509, g-000538 g-000526, g-000551, g-000579, g-000590, g-000445, g-000556, g-000543, g-000501, g-000504, g-000570 PC_ 3 Positive: g-000015, g-000575, g-000483, g-000316, g-000025, g-000364, g-000050, g-000278, g-000443, g-000360 g-000332, g-000124, g-000212, g-000387, g-000536, g-000252, g-000251, g-000321, g-000501, g-000470 g-000582, g-000106, g-000455, g-000368, g-000081, g-000104, g-000437, g-000288, g-000386, g-000317 Negative: g-000211, g-000337, g-000129, g-000185, g-000397, g-000403, g-000253, g-000098, g-000390, g-000303 g-000052, g-000088, g-000463, g-000468, g-000236, g-000209, g-000005, g-000375, g-000342, g-000262 g-000388, g-000091, g-000413, g-000285, g-000003, g-000095, g-000142, g-000205, g-000432, g-000241 PC_ 4 Positive: g-000379, g-000193, g-000212, g-000434, g-000593, g-000513, g-000177, g-000223, g-000069, g-000131 g-000162, g-000345, g-000462, g-000484, g-000448, g-000229, g-000365, g-000302, g-000010, g-000366 g-000051, g-000535, g-000269, g-000270, g-000155, g-000529, g-000373, g-000008, g-000393, g-000306 Negative: g-000334, g-000398, g-000292, g-000095, g-000097, g-000202, g-000382, g-000195, g-000007, g-000079 g-000086, g-000240, g-000263, g-000317, g-000576, g-000557, g-000160, g-000154, g-000214, g-000228 g-000313, g-000053, g-000524, g-000374, g-000568, g-000188, g-000358, g-000528, g-000362, g-000150 PC_ 5 Positive: g-000518, g-000108, g-000186, g-000170, g-000401, g-000337, g-000047, g-000599, g-000432, g-000578 g-000042, g-000065, g-000493, g-000261, g-000533, g-000256, g-000560, g-000596, g-000368, g-000381 g-000535, g-000338, g-000215, g-000159, g-000365, g-000234, g-000173, g-000387, g-000225, g-000272 Negative: g-000451, g-000339, g-000295, g-000328, g-000544, g-000061, g-000227, g-000391, g-000556, g-000237 g-000067, g-000165, g-000449, g-000591, g-000087, g-000129, g-000197, g-000203, g-000487, g-000505 g-000333, g-000029, g-000271, g-000064, g-000583, g-000156, g-000448, g-000153, g-000526, g-000393 Computing nearest neighbor graph Computing SNN Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 1200 Number of edges: 55489 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.5973 Number of communities: 4 Elapsed time: 0 seconds Used resolution for Seurat clusterization is: 0.8 16:10:19 UMAP embedding parameters a = 0.9922 b = 1.112 16:10:19 Read 1200 rows and found 50 numeric columns 16:10:19 Using Annoy for neighbor search, n_neighbors = 30 16:10:19 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 16:10:20 Writing NN index file to temp file /tmp/RtmpXSwR8K/file52724a753cb 16:10:20 Searching Annoy index using 1 thread, search_k = 3000 16:10:20 Annoy recall = 100% 16:10:21 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 16:10:23 Initializing from normalized Laplacian + noise (using RSpectra) 16:10:23 Commencing optimization for 500 epochs, with 42274 positive edges Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 16:10:27 Optimization finished Creating PDF UMAP in file: /tmp/RtmpXSwR8K/test/reclustering/pdf_umap_1.pdf Creating Seurat object: DONE * checking uniformity of cluster '0' of 4 clusters Asked to drop 0 genes and 847 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [353] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.038818359375 | max: 11.109375 | % negative: 5 Only analysis elapsed time: 3.56853985786438 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: 3.73880505561829 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0131180286407471 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0554509162902832 Estimating genes' coex Calculate genes' coex elapsed time: 1.1439700126648 Total calculations elapsed time: 4.95134401321411 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.1183750629425 Total elapsed time: 10.7717299461365 Checking uniformity for the cluster '01_0000' with 353 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0000, with size 353, is uniform 0.83% of the genes is above the given GDI threshold 1.46 GDI 99% quantile is at 1.4439 cluster 01_0000 is uniform * checking uniformity of cluster '1' of 4 clusters Asked to drop 0 genes and 879 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [321] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.0501708984375 | max: 14.515625 | % negative: 8.5 Only analysis elapsed time: 3.6073169708252 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: 3.74658298492432 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00880599021911621 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.049185037612915 Estimating genes' coex Calculate genes' coex elapsed time: 1.13768696784973 Total calculations elapsed time: 4.94226098060608 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.01439499855042 Total elapsed time: 10.7817580699921 Checking uniformity for the cluster '01_0001' with 321 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0001, with size 321, is uniform 0.5% of the genes is above the given GDI threshold 1.46 GDI 99% quantile is at 1.4305 cluster 01_0001 is uniform * checking uniformity of cluster '2' of 4 clusters Asked to drop 0 genes and 905 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [295] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.054443359375 | max: 104 | % negative: 36.5 Only analysis elapsed time: 3.48395299911499 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: 3.68783116340637 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00887393951416016 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0225141048431396 Estimating genes' coex Calculate genes' coex elapsed time: 1.10260987281799 Total calculations elapsed time: 4.82182908058167 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 5.98031687736511 Total elapsed time: 10.6343269348145 Checking uniformity for the cluster '01_0002' with 295 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0002, with size 295, is uniform 0% of the genes is above the given GDI threshold 1.46 GDI 99% quantile is at 1.3925 cluster 01_0002 is uniform * checking uniformity of cluster '3' of 4 clusters Asked to drop 0 genes and 969 cells Cotan analysis functions started Asked to drop 1 genes and 0 cells Genes/cells selection done: dropped [1] genes and [0] cells Working on [599] genes and [231] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:599] to [1:599] Estimate dispersion: DONE dispersion | min: -0.0662841796875 | max: 82.5 | % negative: 33.889816360601 Only analysis elapsed time: 3.43251800537109 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: 3.49391198158264 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00878119468688965 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.025648832321167 Estimating genes' coex Calculate genes' coex elapsed time: 1.13823795318604 Total calculations elapsed time: 4.66657996177673 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 5.7952880859375 Total elapsed time: 10.3692400455475 Checking uniformity for the cluster '01_0003' with 231 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0003, with size 231, is uniform 0% of the genes is above the given GDI threshold 1.46 GDI 99% quantile is at 1.373 cluster 01_0003 is uniform Found 4 uniform and 0 non-uniform clusters NO new possible uniform clusters! Unclustered cell left: 0 The final raw clusterization contains [ 4 ] different clusters: 01_0000, 01_0001, 01_0002, 01_0003 Differential Expression Analysis - START * DEA on cluster '1' * DEA on cluster '2' * DEA on cluster '3' * DEA on cluster '4' Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 3, 2 -> 1, 3 -> 2, 4 -> 4 Cluster, UMAP and Saving the Seurat dataset 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: 0.6846 Number of communities: 4 Elapsed time: 0 seconds 16:11:45 UMAP embedding parameters a = 0.9922 b = 1.112 16:11:45 Read 1200 rows and found 25 numeric columns 16:11:45 Using Annoy for neighbor search, n_neighbors = 30 16:11:45 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 16:11:45 Writing NN index file to temp file /tmp/RtmpXSwR8K/file52755d658d5 16:11:45 Searching Annoy index using 1 thread, search_k = 3000 16:11:45 Annoy recall = 100% 16:11:46 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 16:11:49 Initializing from normalized Laplacian + noise (using RSpectra) 16:11:49 Commencing optimization for 500 epochs, with 43428 positive edges Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 16:11:52 Optimization finished Creating cells' uniform clustering: DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2, 3 -> 3, 4 -> 4 Asked to drop 0 genes and 905 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [295] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.054443359375 | max: 104 | % negative: 36.5 Only analysis elapsed time: 3.62267804145813 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: 3.70413017272949 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00604486465454102 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0134520530700684 Estimating genes' coex Calculate genes' coex elapsed time: 1.18630695343018 Total calculations elapsed time: 4.90993404388428 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.02106189727783 Total elapsed time: 10.7843079566956 Checking uniformity for the cluster 'Cluster_2' with 295 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster Cluster_2, with size 295, is uniform 0% of the genes is above the given GDI threshold 1.46 GDI 99% quantile is at 1.3925 Differential Expression Analysis - START * DEA on cluster '-1' * DEA on cluster '1' * DEA on cluster '2' * DEA on cluster '3' * DEA on cluster '4' Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 2, 2 -> 1, 3 -> 4, 4 -> 3, -1 -> -1 Applied reordering to clusterization is: 1 -> 2, 2 -> 3, 3 -> 1, 4 -> 4, -1 -> -1 Creating cells' uniform clustering: START In iteration 1 the number of cells to re-cluster is 1200 cells belonging to 0 clusters Creating Seurat object: START Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer counts Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Centering and scaling data matrix | | | 0% | |======================================================================| 100% PC_ 1 Positive: g-000558, g-000570, g-000499, g-000504, g-000546, g-000506, g-000503, g-000517, g-000596, g-000528 g-000527, g-000580, g-000592, g-000578, g-000509, g-000488, g-000555, g-000577, g-000534, g-000583 g-000598, g-000535, g-000512, g-000554, g-000519, g-000525, g-000548, g-000544, g-000502, g-000541 Negative: g-000133, g-000007, g-000074, g-000141, g-000057, g-000235, g-000170, g-000019, g-000195, g-000140 g-000183, g-000031, g-000046, g-000178, g-000177, g-000161, g-000157, g-000139, g-000011, g-000135 g-000125, g-000208, g-000061, g-000085, g-000204, g-000104, g-000237, g-000004, g-000038, g-000128 PC_ 2 Positive: g-000039, g-000050, g-000175, g-000078, g-000116, g-000189, g-000135, g-000047, g-000072, g-000087 g-000063, g-000235, g-000066, g-000109, g-000018, g-000074, g-000231, g-000136, g-000034, g-000207 g-000128, g-000167, g-000171, g-000049, g-000182, g-000013, g-000054, g-000062, g-000240, g-000158 Negative: g-000584, g-000583, g-000544, g-000519, g-000575, g-000516, g-000585, g-000486, g-000489, g-000539 g-000484, g-000502, g-000523, g-000595, g-000305, g-000574, g-000599, g-000589, g-000509, g-000538 g-000526, g-000551, g-000579, g-000590, g-000445, g-000556, g-000543, g-000501, g-000504, g-000570 PC_ 3 Positive: g-000015, g-000575, g-000483, g-000316, g-000025, g-000364, g-000050, g-000278, g-000443, g-000360 g-000332, g-000124, g-000212, g-000387, g-000536, g-000252, g-000251, g-000321, g-000501, g-000470 g-000582, g-000106, g-000455, g-000368, g-000081, g-000104, g-000437, g-000288, g-000386, g-000317 Negative: g-000211, g-000337, g-000129, g-000185, g-000397, g-000403, g-000253, g-000098, g-000390, g-000303 g-000052, g-000088, g-000463, g-000468, g-000236, g-000209, g-000005, g-000375, g-000342, g-000262 g-000388, g-000091, g-000413, g-000285, g-000003, g-000095, g-000142, g-000205, g-000432, g-000241 PC_ 4 Positive: g-000379, g-000193, g-000212, g-000434, g-000593, g-000513, g-000177, g-000223, g-000069, g-000131 g-000162, g-000345, g-000462, g-000484, g-000448, g-000229, g-000365, g-000302, g-000010, g-000366 g-000051, g-000535, g-000269, g-000270, g-000155, g-000529, g-000373, g-000008, g-000393, g-000306 Negative: g-000334, g-000398, g-000292, g-000095, g-000097, g-000202, g-000382, g-000195, g-000007, g-000079 g-000086, g-000240, g-000263, g-000317, g-000576, g-000557, g-000160, g-000154, g-000214, g-000228 g-000313, g-000053, g-000524, g-000374, g-000568, g-000188, g-000358, g-000528, g-000362, g-000150 PC_ 5 Positive: g-000518, g-000108, g-000186, g-000170, g-000401, g-000337, g-000047, g-000599, g-000432, g-000578 g-000042, g-000065, g-000493, g-000261, g-000533, g-000256, g-000560, g-000596, g-000368, g-000381 g-000535, g-000338, g-000215, g-000159, g-000365, g-000234, g-000173, g-000387, g-000225, g-000272 Negative: g-000451, g-000339, g-000295, g-000328, g-000544, g-000061, g-000227, g-000391, g-000556, g-000237 g-000067, g-000165, g-000449, g-000591, g-000087, g-000129, g-000197, g-000203, g-000487, g-000505 g-000333, g-000029, g-000271, g-000064, g-000583, g-000156, g-000448, g-000153, g-000526, g-000393 Computing nearest neighbor graph Computing SNN Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 1200 Number of edges: 55489 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.5973 Number of communities: 4 Elapsed time: 0 seconds Used resolution for Seurat clusterization is: 0.8 16:12:16 UMAP embedding parameters a = 0.9922 b = 1.112 16:12:16 Read 1200 rows and found 50 numeric columns 16:12:16 Using Annoy for neighbor search, n_neighbors = 30 16:12:16 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 16:12:17 Writing NN index file to temp file /tmp/RtmpXSwR8K/file5274f736dac 16:12:17 Searching Annoy index using 1 thread, search_k = 3000 16:12:17 Annoy recall = 100% 16:12:18 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 16:12:20 Initializing from normalized Laplacian + noise (using RSpectra) 16:12:20 Commencing optimization for 500 epochs, with 42274 positive edges Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 16:12:25 Optimization finished Creating PDF UMAP in file: /tmp/RtmpXSwR8K/test/reclustering/pdf_umap_1.pdf Creating Seurat object: DONE Using passed in clusterization * checking uniformity of cluster '1' of 2 clusters Asked to drop 0 genes and 600 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [600] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.0386962890625 | max: 19.40625 | % negative: 6.5 Only analysis elapsed time: 3.715576171875 Cotan genes' coex estimation started Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 4.02805685997009 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0124480724334717 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0562169551849365 Estimating genes' coex Calculate genes' coex elapsed time: 1.15701603889465 Total calculations elapsed time: 5.25373792648315 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.30535197257996 Total elapsed time: 11.1394901275635 Checking uniformity for the cluster '01_0001' with 600 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0001, with size 600, is uniform 1% of the genes is above the given GDI threshold 1.46 GDI 99% quantile is at 1.4534 cluster 01_0001 is uniform * checking uniformity of cluster '2' of 2 clusters Asked to drop 0 genes and 600 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [600] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.032958984375 | max: 10.0859375 | % negative: 3.66666666666667 Only analysis elapsed time: 3.71617197990417 Cotan genes' coex estimation started Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 4.08053398132324 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.010822057723999 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0605790615081787 Estimating genes' coex Calculate genes' coex elapsed time: 1.02593994140625 Total calculations elapsed time: 5.17787504196167 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.33345293998718 Total elapsed time: 11.1554269790649 Checking uniformity for the cluster '01_0002' with 600 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0002, with size 600, is uniform 0.5% of the genes is above the given GDI threshold 1.46 GDI 99% quantile is at 1.4378 cluster 01_0002 is uniform Found 2 uniform and 0 non-uniform clusters NO new possible uniform clusters! Unclustered cell left: 0 The final raw clusterization contains [ 2 ] different clusters: 01_0001, 01_0002 Differential Expression Analysis - START * DEA on cluster '1' * DEA on cluster '2' Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Cluster, UMAP and Saving the Seurat dataset 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: 0.6846 Number of communities: 4 Elapsed time: 0 seconds 16:13:06 UMAP embedding parameters a = 0.9922 b = 1.112 16:13:06 Read 1200 rows and found 25 numeric columns 16:13:06 Using Annoy for neighbor search, n_neighbors = 30 16:13:06 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 16:13:06 Writing NN index file to temp file /tmp/RtmpXSwR8K/file5271494c82c 16:13:06 Searching Annoy index using 1 thread, search_k = 3000 16:13:07 Annoy recall = 100% 16:13:08 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 16:13:10 Initializing from normalized Laplacian + noise (using RSpectra) 16:13:10 Commencing optimization for 500 epochs, with 43428 positive edges Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 16:13:14 Optimization finished Creating cells' uniform clustering: DONE findClustersMarkers - START clustersDeltaExpression - START Handling cluster '1' with mean UDE 1.20998115359079 Handling cluster '2' with mean UDE 0.538244816501365 Handling cluster '3' with mean UDE 1.43530796540673 Handling cluster '4' with mean UDE 0.632684489354433 clustersDeltaExpression - 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 findClustersMarkers - START clustersDeltaExpression - START Handling cluster '1' with mean UDE 1.20998115359079 Handling cluster '2' with mean UDE 0.538244816501365 Handling cluster '3' with mean UDE 1.43530796540673 Handling cluster '4' with mean UDE 0.632684489354433 clustersDeltaExpression - 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 findClustersMarkers - START Differential Expression Analysis - START * DEA on cluster '1' * DEA on cluster '2' * DEA on cluster '3' * DEA on cluster '4' Differential Expression Analysis - DONE clustersDeltaExpression - START Handling cluster '1' with mean UDE 1.20998115359079 Handling cluster '2' with mean UDE 0.538244816501365 Handling cluster '3' with mean UDE 1.43530796540673 Handling cluster '4' with mean UDE 0.632684489354433 clustersDeltaExpression - 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] "1" Asked to drop 0 genes and 879 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [321] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.0501708984375 | max: 14.515625 | % negative: 8.5 Only analysis elapsed time: 3.60851883888245 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: 3.73136401176453 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0097510814666748 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0492269992828369 Estimating genes' coex Calculate genes' coex elapsed time: 1.15275406837463 Total calculations elapsed time: 4.94309616088867 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.10493397712708 Total elapsed time: 10.8268959522247 Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE [1] "3" Asked to drop 0 genes and 847 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [353] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.038818359375 | max: 11.109375 | % negative: 5 Only analysis elapsed time: 3.58484196662903 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: 3.77010202407837 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0131499767303467 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.05718994140625 Estimating genes' coex Calculate genes' coex elapsed time: 1.07687902450562 Total calculations elapsed time: 4.91732096672058 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.09704399108887 Total elapsed time: 10.848149061203 Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Initializing `COTAN` meta-data Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Only analysis elapsed time: 4.18590021133423 Cotan genes' coex estimation started Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 4.87909197807312 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00879693031311035 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0672609806060791 Estimating genes' coex Calculate genes' coex elapsed time: 1.15587306022644 Total calculations elapsed time: 6.11102294921875 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 7.16193699836731 Total elapsed time: 12.4720730781555 Calculating gene co-expression space - START Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and genome wide on rows calculating PValues: DONE Number of selected secondary markers: 109 Calculating S: START Calculating S: DONE S matrix sorted Number of columns (V set - secondary markers): 109 Number of rows (U set): 60 Calculating gene co-expression space - DONE Establishing gene clusters - START Calculating gene co-expression space - START Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and genome wide on rows calculating PValues: DONE Number of selected secondary markers: 109 Calculating S: START Calculating S: DONE S matrix sorted Number of columns (V set - secondary markers): 109 Number of rows (U set): 60 Calculating gene co-expression space - DONE Establishing gene clusters - DONE Initializing `COTAN` meta-data Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Cotan genes' coex estimation not requested Total elapsed time: 6.42275094985962 Differential Expression Analysis - START * DEA on cluster '1' * DEA on cluster '2' * DEA on cluster '3' * DEA on cluster '4' Differential Expression Analysis - DONE Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' * Analysis of cluster: '3' * Analysis of cluster: '4' Log Fold Change Analysis - DONE clustersDeltaExpression - START Handling cluster '1' with mean UDE 1.43530796540673 Handling cluster '2' with mean UDE 0.640931107489518 Handling cluster '3' with mean UDE 0.546546914955574 Handling cluster '4' with mean UDE 1.22034802329656 clustersDeltaExpression - DONE In group G1 there are 3 detected over 3 genes In group G2 there are 2 detected over 2 genes In group G3 there are 5 detected over 5 genes Merging cells' uniform clustering: START Start merging nearest clusters: iteration 1 Differential Expression Analysis - START * DEA on cluster '1' * DEA on cluster '2' * DEA on cluster '3' * DEA on cluster '4' Differential Expression Analysis - DONE Clusters pairs for merging: c("1", "2") c("3", "4") c("2", "3") c("2", "4") c("1", "3") c("1", "4") *1_2-merge Asked to drop 0 genes and 626 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [574] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.0340576171875 | max: 10.4375 | % negative: 4.33333333333333 Only analysis elapsed time: 3.66566705703735 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 4.09095501899719 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0101578235626221 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0578081607818604 Estimating genes' coex Calculate genes' coex elapsed time: 1.14677095413208 Total calculations elapsed time: 5.30569195747375 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.46200394630432 Total elapsed time: 11.2921130657196 Checking uniformity for the cluster '1_2-merge' with 574 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 1_2-merge, with size 574, is uniform 0.67% of the genes is above the given GDI threshold 1.46 GDI 99% quantile is at 1.4297 Clusters 1 and 2 can be merged *3_4-merge Asked to drop 0 genes and 574 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [626] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.03839111328125 | max: 17.40625 | % negative: 6.66666666666667 Only analysis elapsed time: 3.74310088157654 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 4.13202381134033 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.010573148727417 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0561819076538086 Estimating genes' coex Calculate genes' coex elapsed time: 1.15691304206848 Total calculations elapsed time: 5.35569190979004 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.4030749797821 Total elapsed time: 11.2578649520874 Checking uniformity for the cluster '3_4-merge' with 626 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 3_4-merge, with size 626, is uniform 1% of the genes is above the given GDI threshold 1.46 GDI 99% quantile is at 1.4544 Clusters 3 and 4 can be merged *Clusters 2 or 3 is now missing due to previous merges: skip. *Clusters 2 or 4 is now missing due to previous merges: skip. *Clusters 1 or 3 is now missing due to previous merges: skip. *Clusters 1 or 4 is now missing due to previous merges: skip. Executed 2 merges out of 6 Start merging nearest clusters: iteration 2 Differential Expression Analysis - START * DEA on cluster '1_2-merge' * DEA on cluster '3_4-merge' Differential Expression Analysis - DONE Clusters pairs for merging: c("1_2-merge", "3_4-merge") *1_2-merge_3_4-merge-merge Asked to drop no genes or cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Only analysis elapsed time: 3.99938893318176 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 4.4415910243988 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00941920280456543 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.076422929763794 Estimating genes' coex Calculate genes' coex elapsed time: 1.18890786170959 Total calculations elapsed time: 5.71634101867676 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.87858700752258 Total elapsed time: 12.0177719593048 Checking uniformity for the cluster '1_2-merge_3_4-merge-merge' with 1200 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 1_2-merge_3_4-merge-merge, with size 1200, is not uniform 22.17% of the genes is above the given GDI threshold 1.46 GDI 99% quantile is at 1.6405 Merging clusters 1_2-merge and 3_4-merge results in a too high GDI None of the 1 nearest cluster pairs could be merged The final merged clusterization contains [2] different clusters: 1_2-merge, 3_4-merge Differential Expression Analysis - START * DEA on cluster '1' * DEA on cluster '2' Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Merging cells' uniform clustering: DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' Log Fold Change Analysis - DONE Asked to drop 0 genes and 626 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [574] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.0340576171875 | max: 10.4375 | % negative: 4.33333333333333 Only analysis elapsed time: 3.61697101593018 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 4.14176511764526 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0116679668426514 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0598108768463135 Estimating genes' coex Calculate genes' coex elapsed time: 1.04981899261475 Total calculations elapsed time: 5.26306295394897 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.39091300964355 Total elapsed time: 11.1569108963013 Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE Asked to drop 0 genes and 574 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [626] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.03839111328125 | max: 17.40625 | % negative: 6.66666666666667 Only analysis elapsed time: 3.69521117210388 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 4.14199995994568 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00860118865966797 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0534429550170898 Estimating genes' coex Calculate genes' coex elapsed time: 1.14201498031616 Total calculations elapsed time: 5.3460590839386 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.41575002670288 Total elapsed time: 11.2764580249786 Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE [ FAIL 0 | WARN 0 | SKIP 0 | PASS 433 ] > > proc.time() user system elapsed 771.614 6.570 782.129
COTAN.Rcheck/COTAN-Ex.timings
name | user | system | elapsed | |
COTAN-Legacy | 0.004 | 0.001 | 0.004 | |
COTANObjectCreation | 12.525 | 0.274 | 12.999 | |
CalculatingCOEX | 73.143 | 1.334 | 76.117 | |
ClustersList | 0.007 | 0.002 | 0.013 | |
GenesStatistics | 14.108 | 0.249 | 14.571 | |
HandleMetaData | 0.103 | 0.011 | 0.116 | |
HandlingClusterizations | 24.911 | 0.539 | 26.452 | |
HandlingConditions | 0.123 | 0.012 | 0.135 | |
HeatmapPlots | 56.363 | 1.647 | 58.424 | |
LoggingFunctions | 0.005 | 0.002 | 0.006 | |
ParametersEstimations | 31.441 | 1.013 | 32.765 | |
RawDataCleaning | 9.212 | 0.167 | 9.387 | |
RawDataGetters | 0.081 | 0.007 | 0.090 | |
UniformClusters | 197.094 | 1.993 | 199.991 | |
getColorsVector | 0.001 | 0.000 | 0.001 | |