Galfrè Silvia Giulia
| Snapshot Date: 2025-02-17 13:40 -0500 (Mon, 17 Feb 2025) |
| git_url: https://git.bioconductor.org/packages/COTAN |
| git_branch: devel |
| git_last_commit: 5b7bd84 |
| git_last_commit_date: 2025-01-27 12:01:10 -0500 (Mon, 27 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-02-18 11:39 -0500 (Tue, 18 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4720 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4482 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4493 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4446 |
| 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 444/2295 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| COTAN 2.7.3 (landing page) Galfrè Silvia Giulia
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 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: 2.7.3 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings COTAN_2.7.3.tar.gz |
| StartedAt: 2025-02-17 21:04:17 -0500 (Mon, 17 Feb 2025) |
| EndedAt: 2025-02-17 21:33:21 -0500 (Mon, 17 Feb 2025) |
| EllapsedTime: 1744.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: COTAN.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings COTAN_2.7.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/COTAN.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘COTAN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COTAN’ version ‘2.7.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘COTAN’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking 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.
Namespace in Imports field not imported from: ‘proj4’
All declared Imports should be used.
Unexported object imported by a ':::' call: ‘ggplot2:::ggname’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
mergeUniformCellsClusters : fromMergedName: warning in
vapply(currentClNames, function(clName, mergedName) {: partial
argument match of 'FUN.VAL' to 'FUN.VALUE'
mergeUniformCellsClusters : fromMergedName: warning in
return(str_detect(mergedName, clName)): partial argument match of
'FUN.VAL' to 'FUN.VALUE'
mergeUniformCellsClusters : fromMergedName: warning in }, FUN.VAL =
logical(1L), mergedClName): partial argument match of 'FUN.VAL' to
'FUN.VALUE'
ECDPlot: no visible binding for global variable ‘.’
GDIPlot: no visible binding for global variable ‘sum.raw.norm’
GDIPlot: no visible binding for global variable ‘GDI’
UMAPPlot: no visible binding for global variable ‘x’
UMAPPlot: no visible binding for global variable ‘y’
UMAPPlot: no visible binding for global variable ‘types’
calculateCoex_Legacy: no visible binding for global variable
‘expectedNN’
calculateCoex_Legacy: no visible binding for global variable
‘expectedNY’
calculateCoex_Legacy: no visible binding for global variable
‘expectedYN’
calculateCoex_Legacy: no visible binding for global variable
‘expectedYY’
calculateCoex_Legacy: no visible binding for global variable
‘observedYY’
calculateCoex_Legacy: no visible binding for global variable ‘.’
calculateG: no visible binding for global variable ‘observedNN’
calculateG: no visible binding for global variable ‘observedNY’
calculateG: no visible binding for global variable ‘observedYN’
calculateG: no visible binding for global variable ‘observedYY’
calculateG: no visible binding for global variable ‘expectedNN’
calculateG: no visible binding for global variable ‘expectedNY’
calculateG: no visible binding for global variable ‘expectedYN’
calculateG: no visible binding for global variable ‘expectedYY’
calculatePartialCoex: no visible binding for global variable
‘expectedNN’
calculatePartialCoex: no visible binding for global variable
‘expectedNY’
calculatePartialCoex: no visible binding for global variable
‘expectedYN’
calculatePartialCoex: no visible binding for global variable
‘expectedYY’
calculatePartialCoex: no visible binding for global variable
‘observedYY’
calculatePartialCoex: no visible binding for global variable ‘.’
cellSizePlot: no visible binding for global variable ‘.’
cellsUniformClustering: no visible binding for global variable
‘objSeurat’
cellsUniformClustering: no visible binding for global variable
‘usedMaxResolution’
cellsUniformClustering: no visible binding for global variable
‘permMap’
checkClusterUniformity: no visible binding for global variable
‘pcaCellsPlot’
checkClusterUniformity: no visible binding for global variable ‘.’
checkClusterUniformity: no visible binding for global variable
‘bGroupGenesPlot’
checkClusterUniformity: no visible binding for global variable
‘UDEPLot’
checkClusterUniformity: no visible binding for global variable ‘nuPlot’
checkClusterUniformity: no visible binding for global variable
‘zoomedNuPlot’
cleanPlots: no visible binding for global variable ‘PC1’
cleanPlots: no visible binding for global variable ‘PC2’
cleanPlots: no visible binding for global variable ‘n’
cleanPlots: no visible binding for global variable ‘means’
cleanPlots: no visible binding for global variable ‘nu’
clustersMarkersHeatmapPlot: no visible binding for global variable
‘condName’
clustersMarkersHeatmapPlot: no visible binding for global variable
‘conditions’
clustersSummaryPlot: no visible binding for global variable ‘keys’
clustersSummaryPlot: no visible binding for global variable ‘values’
clustersSummaryPlot: no visible binding for global variable
‘CellNumber’
clustersSummaryPlot: no visible binding for global variable ‘ExpGenes’
clustersSummaryPlot: no visible binding for global variable ‘Cluster’
clustersSummaryPlot: no visible binding for global variable ‘Condition’
establishGenesClusters: no visible binding for global variable
‘secondaryMarkers’
establishGenesClusters: no visible binding for global variable ‘GCS’
establishGenesClusters: no visible binding for global variable
‘rankGenes’
expectedContingencyTables: no visible binding for global variable
‘expectedN’
expectedPartialContingencyTables: no visible binding for global
variable ‘expectedNN’
expectedPartialContingencyTables: no visible binding for global
variable ‘expectedN’
genesSizePlot: no visible binding for global variable ‘.’
geom_flat_violin : <anonymous>: no visible binding for global variable
‘group’
geom_flat_violin : <anonymous>: no visible binding for global variable
‘y’
geom_flat_violin : <anonymous>: no visible binding for global variable
‘x’
geom_flat_violin : <anonymous>: no visible binding for global variable
‘width’
geom_flat_violin : <anonymous>: no visible binding for global variable
‘violinwidth’
geom_flat_violin : <anonymous>: no visible binding for global variable
‘xmax’
geom_flat_violin : <anonymous>: no visible binding for global variable
‘xminv’
geom_flat_violin : <anonymous>: no visible binding for global variable
‘xmaxv’
heatmapPlot: no visible binding for global variable ‘obj’
heatmapPlot: no visible binding for global variable ‘type’
heatmapPlot: no visible binding for global variable ‘g2’
heatmapPlot: no visible binding for global variable ‘coex’
mergeUniformCellsClusters : fromMergedName: no visible binding for
global variable ‘clName1’
mergeUniformCellsClusters : fromMergedName: no visible binding for
global variable ‘clName2’
mergeUniformCellsClusters : testPairListMerge: no visible binding for
global variable ‘cl1’
mergeUniformCellsClusters : testPairListMerge: no visible binding for
global variable ‘cl2’
mergeUniformCellsClusters : mergeAllClusters : <anonymous>: no visible
binding for global variable ‘clName1’
mergeUniformCellsClusters : mergeAllClusters : <anonymous>: no visible
binding for global variable ‘clName2’
mergeUniformCellsClusters : mergeAllClusters: no visible binding for
global variable ‘clName1’
mergeUniformCellsClusters : mergeAllClusters: no visible binding for
global variable ‘clName2’
mergeUniformCellsClusters: no visible binding for global variable
‘permMap’
mitochondrialPercentagePlot: no visible binding for global variable ‘.’
mitochondrialPercentagePlot: no visible binding for global variable
‘mit.percentage’
observedContingencyTables: no visible binding for global variable
‘observedY’
observedPartialContingencyTables: no visible binding for global
variable ‘observedYY’
observedPartialContingencyTables: no visible binding for global
variable ‘observedY’
scatterPlot: no visible binding for global variable ‘.’
scatterPlot: no visible binding for global variable ‘.x’
calculateCoex,COTAN: no visible binding for global variable ‘useTorch’
coerce,COTAN-scCOTAN: no visible binding for global variable ‘rawNorm’
coerce,COTAN-scCOTAN: no visible binding for global variable ‘nu’
coerce,COTAN-scCOTAN: no visible binding for global variable ‘lambda’
coerce,COTAN-scCOTAN: no visible binding for global variable ‘a’
coerce,COTAN-scCOTAN: no visible binding for global variable ‘hk’
coerce,COTAN-scCOTAN: no visible binding for global variable ‘clusters’
coerce,COTAN-scCOTAN: no visible binding for global variable
‘clusterData’
Undefined global functions or variables:
. .x CellNumber Cluster Condition ExpGenes GCS GDI PC1 PC2 UDEPLot a
bGroupGenesPlot cl1 cl2 clName1 clName2 clusterData clusters coex
condName conditions expectedN expectedNN expectedNY expectedYN
expectedYY g2 group hk keys lambda means mit.percentage n nu nuPlot
obj objSeurat observedNN observedNY observedY observedYN observedYY
pcaCellsPlot permMap rankGenes rawNorm secondaryMarkers sum.raw.norm
type types useTorch usedMaxResolution values violinwidth width x xmax
xmaxv xminv y zoomedNuPlot
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
Conversions.Rd: SingleCellExperiment-class, Assays-class,
SingleCellExperiment
HandlingClusterizations.Rd: umap.defaults
getColorsVector.Rd: brewer.pal, brewer.pal.info
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 205.211 0.854 203.637
CalculatingCOEX 55.257 0.528 54.388
HeatmapPlots 37.223 0.667 36.860
HandlingClusterizations 28.471 0.396 28.803
ParametersEstimations 26.127 0.017 26.129
GenesStatistics 11.508 0.072 11.228
COTAN_ObjectCreation 10.106 0.151 9.923
Conversions 5.685 0.079 5.766
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/COTAN.Rcheck/00check.log’
for details.
COTAN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL COTAN ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘COTAN’ ... ** this is package ‘COTAN’ version ‘2.7.3’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (COTAN)
COTAN.Rcheck/tests/outputTestDatasetCreation.Rout
R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
>
> # Creates the files to be reloaded by the tests for comparisons
> library(zeallot)
>
> outputTestDatasetCreation <- function(testsDir = file.path("tests",
+ "testthat")) {
+ utils::data("test.dataset", package = "COTAN")
+ options(parallelly.fork.enable = TRUE)
+
+ obj <- COTAN(raw = test.dataset)
+ obj <- initializeMetaDataset(obj, GEO = " ",
+ sequencingMethod = "artificial",
+ sampleCondition = "test")
+
+ obj <- proceedToCoex(obj, cores = 6L, saveObj = FALSE)
+ #saveRDS(obj, file = file.path(testsDir,"temp.RDS"))
+
+ cells.names.test <- getCells(obj)[c(1L:10L, 591L:610L, 991L:1000L)]
+ genes.names.test <- getGenes(obj)[c(1L:10L, 291L:310L, 591L: 600L)]
+ saveRDS(cells.names.test, file.path(testsDir, "cells.names.test.RDS"))
+ saveRDS(genes.names.test, file.path(testsDir, "genes.names.test.RDS"))
+
+ dispersion.test <- getDispersion(obj)[genes.names.test]
+ saveRDS(dispersion.test, file.path(testsDir, "dispersion.test.RDS"))
+
+ raw.norm.test <- getNuNormData(obj)[genes.names.test, cells.names.test]
+ saveRDS(raw.norm.test, file.path(testsDir, "raw.norm.test.RDS"))
+
+ coex.test <- getGenesCoex(obj, genes = genes.names.test, zeroDiagonal = FALSE)
+ saveRDS(coex.test, file.path(testsDir, "coex.test.RDS"))
+
+ lambda.test <- getLambda(obj)[genes.names.test]
+ saveRDS(lambda.test, file.path(testsDir, "lambda.test.RDS"))
+
+ GDI.test <- calculateGDI(obj)
+ GDI.test <- GDI.test[genes.names.test, ]
+ saveRDS(GDI.test, file.path(testsDir, "GDI.test.RDS"))
+
+ nu.test <- getNu(obj)[cells.names.test]
+ saveRDS(nu.test, file.path(testsDir, "nu.test.RDS"))
+
+ pval.test <- calculatePValue(obj, geneSubsetCol = genes.names.test)
+ saveRDS(pval.test, file.path(testsDir, "pval.test.RDS"))
+
+ GDIThreshold <- 1.46
+ initialResolution <- 0.8
+ clusters <- cellsUniformClustering(obj, GDIThreshold = GDIThreshold,
+ initialResolution = initialResolution,
+ cores = 6L, saveObj = FALSE)[["clusters"]]
+ saveRDS(clusters, file.path(testsDir, "clusters1.RDS"))
+
+ coexDF <- DEAOnClusters(obj, clusters = clusters)
+ obj <- addClusterization(obj, clName = "clusters",
+ clusters = clusters, coexDF = coexDF)
+
+ saveRDS(coexDF[genes.names.test, ],
+ file.path(testsDir, "coex.test.cluster1.RDS"))
+
+ pvalDF <- pValueFromDEA(coexDF, getNumCells(obj), adjustmentMethod = "none")
+
+ saveRDS(pvalDF[genes.names.test, ],
+ file.path(testsDir, "pval.test.cluster1.RDS"))
+
+ c(mergedClusters, mCoexDF) %<-%
+ mergeUniformCellsClusters(objCOTAN = obj,
+ clusters = NULL,
+ GDIThreshold = GDIThreshold,
+ cores = 6L,
+ distance = "cosine",
+ hclustMethod = "ward.D2",
+ saveObj = FALSE)
+
+ saveRDS(mergedClusters[genes.names.test],
+ file.path(testsDir, "cluster_data_merged.RDS"))
+ }
>
> proc.time()
user system elapsed
0.162 0.026 0.177
COTAN.Rcheck/tests/spelling.Rout
R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> if (requireNamespace("spelling", quietly = TRUE))
+ spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+ skip_on_cran = TRUE)
NULL
>
> proc.time()
user system elapsed
0.132 0.042 0.163
COTAN.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> Sys.setenv(R_TESTS = "")
> library(testthat)
> library(COTAN)
> test_check("COTAN")
Setting new log level to 4
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches 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: 2.18772912025452
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.000946521759033203
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00588798522949219
Estimating genes' coex
Calculate genes' coex elapsed time: 0.697457790374756
Total calculations elapsed time: 2.8920214176178
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: 2.3021252155304
Calculating genes' coex normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.000676393508911133
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00300049781799316
Estimating genes' coex
Calculate genes' coex elapsed time: 0.721793174743652
Total calculations elapsed time: 3.02759528160095
Calculate genes' coex (legacy): DONE
Calculate cells' coex (legacy): START
Retrieving expected cells' contingency table
calculating NN.. done
calculating YN..NY..YY..t().. done
Expected cells' contingency table elapsed time: 2.447594165802
Calculating cells' coex normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.000718355178833008
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00221133232116699
Estimating cells' coex
Calculate cells' coex elapsed time: 0.736026048660278
Total calculations elapsed time: 3.18654990196228
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: 0.619375430892821
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 0.0262702142278251 | 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: 2.54783272743225
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.000540971755981445
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00147891044616699
Estimating genes' coex
Calculate genes' coex elapsed time: 0.852359294891357
Total calculations elapsed time: 3.40221190452576
Calculate genes' coex (legacy): DONE
Calculate cells' coex (legacy): START
Retrieving expected cells' contingency table
calculating NN.. done
calculating YN..NY..YY..t().. done
Expected cells' contingency table elapsed time: 2.35946464538574
Calculating cells' coex normalization factor
Calculate cells' normalization factor elapsed time: 0.00062251091003418
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00158834457397461
Estimating cells' coex
Calculate cells' coex elapsed time: 0.925871849060059
Total calculations elapsed time: 3.28754734992981
Calculate cells' coex (legacy): DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
Calculate genes' partial coex: START
Retrieving expected genes' partial contingency table
calculating partial NN.. done
calculating partial NY..YN..YY.. done
Calculating genes' partial coex normalization factor
Fraction of genes with very low expected contingency tables: 0.325
Retrieving observed genes' yes/yes partial contingency table
calculating partial YY.. done
Estimating genes' partial coex
Calculate genes' partial coex: DONE
Calculate cells' partial coex: START
Retrieving expected cells' partial contingency table
calculating partial NN.. done
calculating partial YN..NY..YY.. done
Calculating cells' partial coex normalization factor
Fraction of genes with very low expected contingency tables: 0
Retrieving observed cells' yes/yes partial contingency table
calculating partial YY.. done
Estimating cells' partial coex
Calculate cells' partial coex: DONE
Asked to drop 2 genes and 0 cells
Asked to drop 0 genes and 4 cells
Asked to drop 2 genes and 2 cells
Attaching package: 'rlang'
The following objects are masked from 'package:testthat':
is_false, is_null, is_true
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
calculating YY.. done
calculating YY.. done
calculating YN..NY..NN..t().. done
Estimate dispersion: START
Effective number of cores used: 1
Executing 3 genes batches from [1:3] to [8:10]
Estimate dispersion: DONE
dispersion | min: 0.9033203125 | max: 4.6796875 | % negative: 10
calculating NN.. done
calculating NN.. done
calculating NY..YN..YY..t().. done
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.26993656158447
Calculating genes' coex normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.000727176666259766
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0014796257019043
Estimating genes' coex
Calculate genes' coex elapsed time: 0.803057909011841
Total calculations elapsed time: 3.07520127296448
Calculate genes' coex (legacy): DONE
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.49435639381409
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.000524759292602539
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00151658058166504
Estimating genes' coex
Calculate genes' coex elapsed time: 0.830608606338501
Total calculations elapsed time: 3.32700634002686
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: 2.15118050575256
Calculating cells' coex normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.000673532485961914
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00144147872924805
Estimating cells' coex
Calculate cells' coex elapsed time: 0.743814706802368
Total calculations elapsed time: 2.89711022377014
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: 2.40497899055481
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00054478645324707
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00147080421447754
Estimating genes' coex
Calculate genes' coex elapsed time: 0.736058235168457
Total calculations elapsed time: 3.14305281639099
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: 3.13976168632507
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: 2.88667583465576
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00595378875732422
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0526266098022461
Estimating genes' coex
Calculate genes' coex elapsed time: 0.855476379394531
Total calculations elapsed time: 3.80073261260986
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.7091326713562
Total elapsed time: 9.42732000350952
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: 3.0154595375061
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: 2.83795261383057
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00542616844177246
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0496931076049805
Estimating genes' coex
Calculate genes' coex elapsed time: 0.79707932472229
Total calculations elapsed time: 3.69015121459961
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.46314764022827
Total elapsed time: 9.0285336971283
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: 2.84527158737183
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.57892560958862
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00498843193054199
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.049102783203125
Estimating genes' coex
Calculate genes' coex elapsed time: 0.712022542953491
Total calculations elapsed time: 3.34503936767578
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.11822366714478
Total elapsed time: 8.55286264419556
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: 2.94204306602478
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.6989688873291
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00503849983215332
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0494263172149658
Estimating genes' coex
Calculate genes' coex elapsed time: 0.759351015090942
Total calculations elapsed time: 3.51278471946716
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.28794598579407
Total elapsed time: 8.75130796432495
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: 4.48309779167175
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: 2.28284287452698
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00481605529785156
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00670003890991211
Estimating genes' coex
Calculate genes' coex elapsed time: 0.779562473297119
Total calculations elapsed time: 3.07392144203186
Calculate genes' coex (legacy): DONE
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.38005781173706
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00502228736877441
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00662398338317871
Estimating genes' coex
Calculate genes' coex elapsed time: 0.74958348274231
Total calculations elapsed time: 3.14128756523132
Calculate genes' coex (legacy): DONE
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.22164916992188
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0052187442779541
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00693392753601074
Estimating genes' coex
Calculate genes' coex elapsed time: 0.760104417800903
Total calculations elapsed time: 2.99390625953674
Calculate genes' coex (legacy): DONE
Hangling COTAN object with condition: test
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and on a set of genes on rows
calculating PValues: DONE
Handling genes type: G2
Handling genes type: G3
Initializing `COTAN` meta-data
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
PCA: START
PCA: DONE
Hierarchical clustering: START
Hierarchical clustering: DONE
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Cotan genes' coex estimation not requested
Total elapsed time: 7.7397403717041
Saving elaborated data locally at: /tmp/RtmpFHc6XX/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-000334, g-000398, g-000292, g-000095, g-000097, g-000202, g-000382, g-000195, g-000007, g-000079
g-000086, g-000240, g-000263, g-000317, g-000576, g-000557, g-000160, g-000154, g-000214, g-000228
g-000313, g-000053, g-000524, g-000374, g-000568, g-000188, g-000358, g-000528, g-000362, g-000150
Negative: g-000379, g-000193, g-000212, g-000434, g-000593, g-000513, g-000177, g-000223, g-000069, g-000131
g-000162, g-000345, g-000462, g-000484, g-000448, g-000229, g-000365, g-000302, g-000010, g-000366
g-000051, g-000535, g-000269, g-000270, g-000155, g-000529, g-000373, g-000008, g-000393, g-000306
PC_ 5
Positive: g-000451, g-000339, g-000295, g-000328, g-000544, g-000061, g-000227, g-000391, g-000556, g-000237
g-000067, g-000165, g-000449, g-000591, g-000087, g-000129, g-000197, g-000203, g-000487, g-000505
g-000333, g-000029, g-000271, g-000064, g-000583, g-000156, g-000448, g-000153, g-000526, g-000393
Negative: g-000518, g-000108, g-000186, g-000170, g-000401, g-000337, g-000047, g-000599, g-000432, g-000578
g-000042, g-000065, g-000493, g-000261, g-000533, g-000256, g-000560, g-000596, g-000368, g-000381
g-000535, g-000338, g-000215, g-000159, g-000365, g-000234, g-000173, g-000387, g-000225, g-000272
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 1200
Number of edges: 55489
Running Louvain algorithm with multilevel refinement...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5973
Number of communities: 4
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 0.8
21:20:34 UMAP embedding parameters a = 0.9922 b = 1.112
21:20:34 Read 1200 rows and found 50 numeric columns
21:20:34 Using Annoy for neighbor search, n_neighbors = 30
21:20:34 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
21:20:34 Writing NN index file to temp file /tmp/RtmpFHc6XX/file22df7f1e4b1b6d
21:20:34 Searching Annoy index using 1 thread, search_k = 3000
21:20:35 Annoy recall = 100%
21:20:36 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
21:20:37 Initializing from normalized Laplacian + noise (using RSpectra)
21:20:37 Commencing optimization for 500 epochs, with 42274 positive edges
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
21:20:40 Optimization finished
Creating PDF UMAP in file: /tmp/RtmpFHc6XX/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: 2.48993921279907
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.51116728782654
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00507426261901855
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0384399890899658
Estimating genes' coex
Calculate genes' coex elapsed time: 0.80353832244873
Total calculations elapsed time: 3.35821986198425
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.17788529396057
Total elapsed time: 8.32002425193787
Checking uniformity for the cluster '01_0000' with 353 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0000, with size 353, is uniform
check.isCheckAbove = 0, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0.00833333333333333, check.thresholdRank = 0, check.quantileAtRatio = 1.44390094359269, check.quantileAtRank = NaN, isUniform = 1, clusterSize = 353
cluster 01_0000 is uniform
* checking uniformity of cluster '1' of 4 clusters
Asked to drop 0 genes and 879 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [321] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.0501708984375 | max: 14.515625 | % negative: 8.5
Only analysis elapsed time: 2.77443599700928
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.84135365486145
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00578975677490234
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.035261869430542
Estimating genes' coex
Calculate genes' coex elapsed time: 0.836173534393311
Total calculations elapsed time: 3.71857881546021
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.56339836120605
Total elapsed time: 9.0588583946228
Checking uniformity for the cluster '01_0001' with 321 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0001, with size 321, is uniform
check.isCheckAbove = 0, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0.005, check.thresholdRank = 0, check.quantileAtRatio = 1.43049825920349, check.quantileAtRank = NaN, isUniform = 1, clusterSize = 321
cluster 01_0001 is uniform
* checking uniformity of cluster '2' of 4 clusters
Asked to drop 0 genes and 905 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [295] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.054443359375 | max: 104 | % negative: 36.5
Only analysis elapsed time: 2.7949206829071
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: 3.02669239044189
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00676727294921875
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0173516273498535
Estimating genes' coex
Calculate genes' coex elapsed time: 0.877440690994263
Total calculations elapsed time: 3.92825198173523
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.97616052627563
Total elapsed time: 9.56194376945496
Checking uniformity for the cluster '01_0002' with 295 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0002, with size 295, is uniform
check.isCheckAbove = 0, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0, check.thresholdRank = 0, check.quantileAtRatio = 1.39247518634894, check.quantileAtRank = NaN, isUniform = 1, clusterSize = 295
cluster 01_0002 is uniform
* checking uniformity of cluster '3' of 4 clusters
Asked to drop 0 genes and 969 cells
Cotan analysis functions started
Asked to drop 1 genes and 0 cells
Genes/cells selection done: dropped [1] genes and [0] cells
Working on [599] genes and [231] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:599] to [1:599]
Estimate dispersion: DONE
dispersion | min: -0.0662841796875 | max: 82.5 | % negative: 33.889816360601
Only analysis elapsed time: 2.78779363632202
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.76960611343384
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0061182975769043
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0171747207641602
Estimating genes' coex
Calculate genes' coex elapsed time: 0.849805116653442
Total calculations elapsed time: 3.64270424842834
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.50337648391724
Total elapsed time: 9.08532643318176
Checking uniformity for the cluster '01_0003' with 231 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0003, with size 231, is uniform
check.isCheckAbove = 0, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0, check.thresholdRank = 0, check.quantileAtRatio = 1.37302163462669, check.quantileAtRank = NaN, isUniform = 1, clusterSize = 231
cluster 01_0003 is uniform
Found 4 uniform and 0 non-uniform clusters
NO new possible uniform clusters! Unclustered cell left: 0
The final raw clusterization contains [ 4 ] different clusters: 01_0000, 01_0001, 01_0002, 01_0003
Differential Expression Analysis - START
* DEA on cluster '1' with 353 cells
* DEA on cluster '2' with 321 cells
* DEA on cluster '3' with 295 cells
* DEA on cluster '4' with 231 cells
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1 -> 3, 2 -> 1, 3 -> 2, 4 -> 4
Creating cells' uniform clustering: DONE
Applied reordering to clusterization is:
1 -> 1, 2 -> 2, 3 -> 3, 4 -> 4
Asked to drop 0 genes and 905 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [295] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.054443359375 | max: 104 | % negative: 36.5
Only analysis elapsed time: 2.87963128089905
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.74953007698059
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00555014610290527
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0167942047119141
Estimating genes' coex
Calculate genes' coex elapsed time: 0.884064674377441
Total calculations elapsed time: 3.65593910217285
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.4776771068573
Total elapsed time: 9.14607882499695
Checking uniformity for the cluster 'Cluster_2' with 295 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster Cluster_2, with size 295, is uniform
firstCheck.isCheckAbove = 0, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0416666666666667, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.29139209027198, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = 1, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.035, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.34700400911787, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = 0, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00833333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.39247518634894, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = 0, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 5, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.4279762218014, isUniform = 1, clusterSize = 295
Differential Expression Analysis - START
* DEA on cluster '-1' with 50 cells
* DEA on cluster '1' with 321 cells
* DEA on cluster '2' with 245 cells
* DEA on cluster '3' with 353 cells
* DEA on cluster '4' with 231 cells
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1 -> 2, 2 -> 1, 3 -> 4, 4 -> 3, -1 -> -1
Applied reordering to clusterization is:
1 -> 2, 2 -> 3, 3 -> 1, 4 -> 4, -1 -> -1
Creating cells' uniform clustering: START
In iteration 1 the number of cells to re-cluster is 1200 cells belonging to 0 clusters
Creating Seurat object: START
Normalizing layer: counts
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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: 3.08925437927246
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: 2.72067403793335
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00580334663391113
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0495784282684326
Estimating genes' coex
Calculate genes' coex elapsed time: 0.806178092956543
Total calculations elapsed time: 3.58223390579224
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.42802906036377
Total elapsed time: 9.17230319976807
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
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-000334, g-000398, g-000292, g-000095, g-000097, g-000202, g-000382, g-000195, g-000007, g-000079
g-000086, g-000240, g-000263, g-000317, g-000576, g-000557, g-000160, g-000154, g-000214, g-000228
g-000313, g-000053, g-000524, g-000374, g-000568, g-000188, g-000358, g-000528, g-000362, g-000150
Negative: g-000379, g-000193, g-000212, g-000434, g-000593, g-000513, g-000177, g-000223, g-000069, g-000131
g-000162, g-000345, g-000462, g-000484, g-000448, g-000229, g-000365, g-000302, g-000010, g-000366
g-000051, g-000535, g-000269, g-000270, g-000155, g-000529, g-000373, g-000008, g-000393, g-000306
PC_ 5
Positive: g-000451, g-000339, g-000295, g-000328, g-000544, g-000061, g-000227, g-000391, g-000556, g-000237
g-000067, g-000165, g-000449, g-000591, g-000087, g-000129, g-000197, g-000203, g-000487, g-000505
g-000333, g-000029, g-000271, g-000064, g-000583, g-000156, g-000448, g-000153, g-000526, g-000393
Negative: g-000518, g-000108, g-000186, g-000170, g-000401, g-000337, g-000047, g-000599, g-000432, g-000578
g-000042, g-000065, g-000493, g-000261, g-000533, g-000256, g-000560, g-000596, g-000368, g-000381
g-000535, g-000338, g-000215, g-000159, g-000365, g-000234, g-000173, g-000387, g-000225, g-000272
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 1200
Number of edges: 55489
Running Louvain algorithm with multilevel refinement...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5973
Number of communities: 4
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 0.8
21:22:12 UMAP embedding parameters a = 0.9922 b = 1.112
21:22:12 Read 1200 rows and found 50 numeric columns
21:22:12 Using Annoy for neighbor search, n_neighbors = 30
21:22:12 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
21:22:12 Writing NN index file to temp file /tmp/RtmpFHc6XX/file22df7f2a1cd5b3
21:22:12 Searching Annoy index using 1 thread, search_k = 3000
21:22:13 Annoy recall = 100%
21:22:14 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
21:22:15 Initializing from normalized Laplacian + noise (using RSpectra)
21:22:15 Commencing optimization for 500 epochs, with 42246 positive edges
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
21:22:18 Optimization finished
Creating PDF UMAP in file: /tmp/RtmpFHc6XX/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: 2.566237449646
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: 2.49613308906555
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00557756423950195
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0372514724731445
Estimating genes' coex
Calculate genes' coex elapsed time: 0.824793100357056
Total calculations elapsed time: 3.36375522613525
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.18122982978821
Total elapsed time: 8.33183145523071
Checking uniformity for the cluster '01_0001' with 600 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0001, with size 600, is uniform
firstCheck.isCheckAbove = 0, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0383333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.38474391612667, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = 1, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.035, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42418110276821, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = 0, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00666666666666667, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.45338035249414, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = 0, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 4, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.51521594648007, isUniform = 1, clusterSize = 600
cluster 01_0001 is uniform
* checking uniformity of cluster '2' of 2 clusters
Asked to drop 0 genes and 600 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [600] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.032958984375 | max: 10.0859375 | % negative: 3.66666666666667
Only analysis elapsed time: 2.61008191108704
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: 2.63826560974121
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00504660606384277
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0410563945770264
Estimating genes' coex
Calculate genes' coex elapsed time: 0.862200736999512
Total calculations elapsed time: 3.54656934738159
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.38567280769348
Total elapsed time: 8.51735520362854
Checking uniformity for the cluster '01_0002' with 600 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0002, with size 600, is uniform
firstCheck.isCheckAbove = 0, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0366666666666667, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.37665544944664, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = 1, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.0316666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42305229982216, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = 0, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00333333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.43783135828069, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = 0, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 2, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.50182972335853, isUniform = 1, clusterSize = 600
cluster 01_0002 is uniform
Found 2 uniform and 0 non-uniform clusters
NO new possible uniform clusters! Unclustered cell left: 0
The final raw clusterization contains [ 2 ] different clusters: 01_0001, 01_0002
Differential Expression Analysis - START
* DEA on cluster '1' with 600 cells
* DEA on cluster '2' with 600 cells
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1 -> 1, 2 -> 2
Creating cells' uniform clustering: DONE
findClustersMarkers - START
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
* Analysis of cluster: '3'
* Analysis of cluster: '4'
Log Fold Change Analysis - DONE
findClustersMarkers - DONE
findClustersMarkers - START
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
* Analysis of cluster: '3'
* Analysis of cluster: '4'
Log Fold Change Analysis - DONE
findClustersMarkers - DONE
findClustersMarkers - START
Differential Expression Analysis - START
* DEA on cluster '1' with 321 cells
* DEA on cluster '2' with 295 cells
* DEA on cluster '3' with 353 cells
* DEA on cluster '4' with 231 cells
Differential Expression Analysis - DONE
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
* Analysis of cluster: '3'
* Analysis of cluster: '4'
Log Fold Change Analysis - DONE
findClustersMarkers - DONE
[1] "Tested cluster: 1"
Asked to drop 0 genes and 879 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [321] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.0501708984375 | max: 14.515625 | % negative: 8.5
Only analysis elapsed time: 2.56598353385925
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.39559054374695
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00509858131408691
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.03413987159729
Estimating genes' coex
Calculate genes' coex elapsed time: 0.717602968215942
Total calculations elapsed time: 3.15243196487427
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 3.8859076499939
Total elapsed time: 8.05392956733704
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
[1] "Tested cluster: 3"
Asked to drop 0 genes and 847 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [353] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.038818359375 | max: 11.109375 | % negative: 5
Only analysis elapsed time: 2.55597376823425
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.48345804214478
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00509095191955566
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0381643772125244
Estimating genes' coex
Calculate genes' coex elapsed time: 0.872625350952148
Total calculations elapsed time: 3.399338722229
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.20124673843384
Total elapsed time: 8.34627413749695
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Initializing `COTAN` meta-data
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Cotan genes' coex estimation not requested
Total elapsed time: 5.53499960899353
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-000334, g-000398, g-000292, g-000095, g-000097, g-000202, g-000382, g-000195, g-000007, g-000079
g-000086, g-000240, g-000263, g-000317, g-000576, g-000557, g-000160, g-000154, g-000214, g-000228
g-000313, g-000053, g-000524, g-000374, g-000568, g-000188, g-000358, g-000528, g-000362, g-000150
Negative: g-000379, g-000193, g-000212, g-000434, g-000593, g-000513, g-000177, g-000223, g-000069, g-000131
g-000162, g-000345, g-000462, g-000484, g-000448, g-000229, g-000365, g-000302, g-000010, g-000366
g-000051, g-000535, g-000269, g-000270, g-000155, g-000529, g-000373, g-000008, g-000393, g-000306
PC_ 5
Positive: g-000451, g-000339, g-000295, g-000328, g-000544, g-000061, g-000227, g-000391, g-000556, g-000237
g-000067, g-000165, g-000449, g-000591, g-000087, g-000129, g-000197, g-000203, g-000487, g-000505
g-000333, g-000029, g-000271, g-000064, g-000583, g-000156, g-000448, g-000153, g-000526, g-000393
Negative: g-000518, g-000108, g-000186, g-000170, g-000401, g-000337, g-000047, g-000599, g-000432, g-000578
g-000042, g-000065, g-000493, g-000261, g-000533, g-000256, g-000560, g-000596, g-000368, g-000381
g-000535, g-000338, g-000215, g-000159, g-000365, g-000234, g-000173, g-000387, g-000225, g-000272
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 1200
Number of edges: 55489
Running Louvain algorithm with multilevel refinement...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5973
Number of communities: 4
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 0.8
21:23:33 UMAP embedding parameters a = 0.9922 b = 1.112
21:23:33 Read 1200 rows and found 50 numeric columns
21:23:33 Using Annoy for neighbor search, n_neighbors = 30
21:23:33 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
21:23:33 Writing NN index file to temp file /tmp/RtmpFHc6XX/file22df7f1ad9f203
21:23:33 Searching Annoy index using 1 thread, search_k = 3000
21:23:34 Annoy recall = 100%
21:23:35 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
21:23:36 Initializing from normalized Laplacian + noise (using RSpectra)
21:23:36 Commencing optimization for 500 epochs, with 42274 positive edges
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
21:23:39 Optimization finished
Creating Seurat object: DONE
Clusterizations found: RNA_snn_res.0.8, seurat_clusters
Conditions found: orig.ident
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Cotan genes' coex estimation not requested
Total elapsed time: 5.74256563186646
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: 3.1741988658905
Cotan genes' coex estimation started
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.05298495292664
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00523042678833008
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0499405860900879
Estimating genes' coex
Calculate genes' coex elapsed time: 0.868083000183105
Total calculations elapsed time: 3.97623896598816
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.78573703765869
Total elapsed time: 9.6658763885498
Calculating gene co-expression space - START
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
calculating PValues: DONE
Number of selected secondary markers: 6
Calculating S: START
Calculating S: DONE
S matrix sorted
Number of columns (V set - secondary markers): 6
Number of rows (U set): 60
Calculating gene co-expression space - DONE
Calculating gene co-expression space - START
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
calculating PValues: DONE
Number of selected secondary markers: 109
Calculating S: START
Calculating S: DONE
S matrix sorted
Number of columns (V set - secondary markers): 109
Number of rows (U set): 60
Calculating gene co-expression space - DONE
Establishing gene clusters - START
Calculating gene co-expression space - START
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
calculating PValues: DONE
Number of selected secondary markers: 109
Calculating S: START
Calculating S: DONE
S matrix sorted
Number of columns (V set - secondary markers): 109
Number of rows (U set): 60
Calculating gene co-expression space - DONE
Establishing gene clusters - DONE
Initializing `COTAN` meta-data
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Cotan genes' coex estimation not requested
Total elapsed time: 5.48547720909119
Differential Expression Analysis - START
* DEA on cluster '1' with 353 cells
* DEA on cluster '2' with 221 cells
* DEA on cluster '3' with 315 cells
* DEA on cluster '4' with 311 cells
Differential Expression Analysis - DONE
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
* Analysis of cluster: '3'
* Analysis of cluster: '4'
Log Fold Change Analysis - DONE
clustersDeltaExpression - START
Handling cluster '1' with mean UDE 1.43530796540674
Handling cluster '2' with mean UDE 0.640931107489519
Handling cluster '3' with mean UDE 0.546546914955575
Handling cluster '4' with mean UDE 1.22034802329657
clustersDeltaExpression - DONE
In group G1 there are 3 detected over 3 genes
In group G2 there are 2 detected over 2 genes
In group G3 there are 5 detected over 5 genes
Merging cells' uniform clustering: START
The merge algorithm will use 2 passes
Start merging nearest clusters - the main threshold is: 1.297
Start merging nearest clusters: iteration 1
Differential Expression Analysis - START
* DEA on cluster '1' with 353 cells
* DEA on cluster '2' with 221 cells
* DEA on cluster '3' with 315 cells
* DEA on cluster '4' with 311 cells
Differential Expression Analysis - DONE
Updating check results for the 0 already tested pairs to align to new checker
2 new clusters pairs to be tested for merging:
c("1", "2") c("3", "4")
*1_2-merge
Asked to drop 0 genes and 626 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [574] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.0340576171875 | max: 10.4375 | % negative: 4.33333333333333
Only analysis elapsed time: 2.73656105995178
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.74495434761047
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00506687164306641
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0405364036560059
Estimating genes' coex
Calculate genes' coex elapsed time: 0.855724334716797
Total calculations elapsed time: 3.64628195762634
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.45429754257202
Total elapsed time: 8.81504082679749
Checking uniformity for the cluster '1_2-merge' with 574 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 1_2-merge, with size 574, is not uniform
firstCheck.isCheckAbove = 0, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.326666666666667, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.37902213691275, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = 1, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.28, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.41724738266283, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = 0, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.0333333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.42971854140312, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = 0, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 20, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.5067755752749, isUniform = 0, clusterSize = 574
Clusters 1 and 2 cannot be merged
*3_4-merge
Asked to drop 0 genes and 574 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [626] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.03839111328125 | max: 17.40625 | % negative: 6.66666666666667
Only analysis elapsed time: 2.68680381774902
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.62393951416016
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00537681579589844
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0372278690338135
Estimating genes' coex
Calculate genes' coex elapsed time: 0.85898494720459
Total calculations elapsed time: 3.52552914619446
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.36231923103333
Total elapsed time: 8.65788912773132
Checking uniformity for the cluster '3_4-merge' with 626 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 3_4-merge, with size 626, is not uniform
firstCheck.isCheckAbove = 0, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.248333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.38846117443461, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = 1, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.218333333333333, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42066795244751, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = 0, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.0366666666666667, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.45442688129939, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = 0, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 22, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.52592182249635, isUniform = 0, clusterSize = 626
Clusters 3 and 4 cannot be merged
Finished the first batch - no merges were executed
Start merging nearest clusters: iteration 2
Differential Expression Analysis - START
* DEA on cluster '1' with 353 cells
* DEA on cluster '2' with 221 cells
* DEA on cluster '3' with 315 cells
* DEA on cluster '4' with 311 cells
Differential Expression Analysis - DONE
Updating check results for the 2 already tested pairs to align to new checker
2 new clusters pairs to be tested for merging:
c("2", "3") c("2", "4")
*2_3-merge
Asked to drop 0 genes and 664 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [536] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.0390625 | max: 12.59375 | % negative: 9.16666666666667
Only analysis elapsed time: 2.66329216957092
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.65926122665405
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0051119327545166
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0278308391571045
Estimating genes' coex
Calculate genes' coex elapsed time: 0.808969259262085
Total calculations elapsed time: 3.50117325782776
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.31987857818604
Total elapsed time: 8.52391242980957
Checking uniformity for the cluster '2_3-merge' with 536 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 2_3-merge, with size 536, is not uniform
firstCheck.isCheckAbove = 0, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.29, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.39921369800378, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = 1, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.251666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.45276697088286, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = 0, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.05, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.49016449535422, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = 0, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 30, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.54477108741147, isUniform = 0, clusterSize = 536
Clusters 2 and 3 cannot be merged
*2_4-merge
Asked to drop 0 genes and 668 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [532] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.04754638671875 | max: 10.234375 | % negative: 5
Only analysis elapsed time: 2.76538825035095
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.85047745704651
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0056765079498291
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0383098125457764
Estimating genes' coex
Calculate genes' coex elapsed time: 0.867518186569214
Total calculations elapsed time: 3.76198196411133
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.63642907142639
Total elapsed time: 8.99588322639465
Checking uniformity for the cluster '2_4-merge' with 532 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 2_4-merge, with size 532, is not uniform
firstCheck.isCheckAbove = 0, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.39, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.51012921768223, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = 1, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.361666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.55599610798341, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = 0, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.181666666666667, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.59088431608469, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = 0, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 109, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.68475283375668, isUniform = 0, clusterSize = 532
Clusters 2 and 4 cannot be merged
No clusters will be merged
None of the remaining tested cluster pairs could be merged
Executed all merges for threshold 1.297 out of 4 checks
Start merging nearest clusters - the main threshold is: 1.397
Start merging nearest clusters: iteration 3
Differential Expression Analysis - START
* DEA on cluster '1' with 353 cells
* DEA on cluster '2' with 221 cells
* DEA on cluster '3' with 315 cells
* DEA on cluster '4' with 311 cells
Differential Expression Analysis - DONE
Updating check results for the 4 already tested pairs to align to new checker
2 new clusters pairs to be tested for merging:
c("1", "3") c("1", "4")
*1_3-merge
Asked to drop 0 genes and 532 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [668] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.046630859375 | max: 9.03515625 | % negative: 1.33333333333333
Only analysis elapsed time: 3.01093673706055
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.61064052581787
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0051424503326416
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0415253639221191
Estimating genes' coex
Calculate genes' coex elapsed time: 0.833818197250366
Total calculations elapsed time: 3.491126537323
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.37293577194214
Total elapsed time: 9.08834195137024
Checking uniformity for the cluster '1_3-merge' with 668 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 1_3-merge, with size 668, is not uniform
firstCheck.isCheckAbove = 0, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.33, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.5749237074053, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = 1, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.31, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.6368755707341, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = 0, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.128333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.65704996173771, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = 0, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 77, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.68881338289977, isUniform = 0, clusterSize = 668
Clusters 1 and 3 cannot be merged
*1_4-merge
Asked to drop 0 genes and 536 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [664] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.0164794921875 | max: 5.5595703125 | % negative: 0.166666666666667
Only analysis elapsed time: 2.95175981521606
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.91402268409729
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00522279739379883
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0455937385559082
Estimating genes' coex
Calculate genes' coex elapsed time: 0.822028398513794
Total calculations elapsed time: 3.78686761856079
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.627286195755
Total elapsed time: 9.5294291973114
Checking uniformity for the cluster '1_4-merge' with 664 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 1_4-merge, with size 664, is not uniform
firstCheck.isCheckAbove = 0, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.348333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.53527735568616, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = 1, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.316666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.55951216335001, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = 0, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.0983333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.59105696847609, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = 0, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 59, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.64605433203111, isUniform = 0, clusterSize = 664
Clusters 1 and 4 cannot be merged
Clusters 2 and 1 will be merged
Clusters 3 and 4 will be merged
Executed 2 merges
Start merging nearest clusters: iteration 4
Differential Expression Analysis - START
* DEA on cluster '1_2-merge' with 574 cells
* DEA on cluster '3_4-merge' with 626 cells
Differential Expression Analysis - DONE
Updating check results for the 6 already tested pairs to align to new checker
1 new clusters pairs to be tested for merging:
c("1_2-merge", "3_4-merge")
*1_2-merge_3_4-merge-merge
Asked to drop no genes or cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 3.33870935440063
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: 3.12323784828186
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00522351264953613
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0495729446411133
Estimating genes' coex
Calculate genes' coex elapsed time: 0.86106014251709
Total calculations elapsed time: 4.0390944480896
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.92726635932922
Total elapsed time: 9.99087572097778
Checking uniformity for the cluster '1_2-merge_3_4-merge-merge' with 1200 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 1_2-merge_3_4-merge-merge, with size 1200, is not uniform
firstCheck.isCheckAbove = 0, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.415, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.57017498537933, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = 1, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.388333333333333, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.61240081401504, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = 0, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.15, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.64046660675367, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = 0, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 90, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.66512085964758, isUniform = 0, clusterSize = 1200
Clusters 1_2-merge and 3_4-merge cannot be merged
No clusters will be merged
None of the remaining tested cluster pairs could be merged
Executed all merges for threshold 1.397 out of 7 checks
The final merged clusterization contains [2] different clusters: 1_2-merge, 3_4-merge
Differential Expression Analysis - START
* DEA on cluster '1' with 574 cells
* DEA on cluster '2' with 626 cells
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1 -> 1, 2 -> 2
Merging cells' uniform clustering: DONE
Applied reordering to clusterization is:
1 -> 1, 2 -> 2
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
Log Fold Change Analysis - DONE
Asked to drop 0 genes and 626 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [574] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.0340576171875 | max: 10.4375 | % negative: 4.33333333333333
Only analysis elapsed time: 2.74191308021545
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.74195408821106
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00535130500793457
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0407543182373047
Estimating genes' coex
Calculate genes' coex elapsed time: 0.82560658454895
Total calculations elapsed time: 3.61366629600525
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.44095253944397
Total elapsed time: 9.03286743164062
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: 2.82440876960754
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.78863048553467
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00555515289306641
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0376989841461182
Estimating genes' coex
Calculate genes' coex elapsed time: 0.854038238525391
Total calculations elapsed time: 3.68592286109924
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.59767699241638
Total elapsed time: 9.14634203910828
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 506 ]
>
> proc.time()
user system elapsed
685.255 3.925 683.575
COTAN.Rcheck/COTAN-Ex.timings
| name | user | system | elapsed | |
| COTAN_Legacy | 0.003 | 0.001 | 0.004 | |
| COTAN_ObjectCreation | 10.106 | 0.151 | 9.923 | |
| CalculatingCOEX | 55.257 | 0.528 | 54.388 | |
| ClustersList | 0.005 | 0.003 | 0.007 | |
| Conversions | 5.685 | 0.079 | 5.766 | |
| GenesStatistics | 11.508 | 0.072 | 11.228 | |
| HandleMetaData | 0.066 | 0.001 | 0.067 | |
| HandlingClusterizations | 28.471 | 0.396 | 28.803 | |
| HandlingConditions | 0.094 | 0.000 | 0.094 | |
| HeatmapPlots | 37.223 | 0.667 | 36.860 | |
| LoggingFunctions | 0.001 | 0.001 | 0.002 | |
| ParametersEstimations | 26.127 | 0.017 | 26.129 | |
| RawDataCleaning | 4.689 | 0.035 | 4.646 | |
| RawDataGetters | 0.090 | 0.001 | 0.091 | |
| UniformClusters | 205.211 | 0.854 | 203.637 | |
| getColorsVector | 0.001 | 0.000 | 0.001 | |