Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-16 11:40 -0400 (Fri, 16 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4420 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
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 672/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
EWCE 1.13.1 (landing page) Alan Murphy
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the EWCE package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EWCE.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: EWCE |
Version: 1.13.1 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:EWCE.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings EWCE_1.13.1.tar.gz |
StartedAt: 2024-08-16 00:37:39 -0400 (Fri, 16 Aug 2024) |
EndedAt: 2024-08-16 00:59:00 -0400 (Fri, 16 Aug 2024) |
EllapsedTime: 1280.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: EWCE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:EWCE.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings EWCE_1.13.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/EWCE.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'EWCE/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'EWCE' version '1.13.1' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'EWCE' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... NOTE checkRd: (-1) compute_gene_scores.Rd:42: Lost braces in \itemize; meant \describe ? checkRd: (-1) compute_gene_scores.Rd:43: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:186-187: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:188-189: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:190-192: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:52-55: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:56-58: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:59-61: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:62-64: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:65-68: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:69-74: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:108: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:109-110: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:111: Lost braces 111 | \item{code{list} : \cr}{A \code{list} or character \code{vector}.} | ^ checkRd: (-1) drop_uninformative_genes.Rd:111: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:124: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:125: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:126-127: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:132: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:133: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:134-136: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:137-138: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:139-140: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:159-162: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:163-166: Lost braces in \itemize; meant \describe ? checkRd: (-1) drop_uninformative_genes.Rd:167-170: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:46-49: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:50-52: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:53-55: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:56-58: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:59-62: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:63-68: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:110: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:111-112: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:113: Lost braces 113 | \item{code{list} : \cr}{A \code{list} or character \code{vector}.} | ^ checkRd: (-1) extract_matrix.Rd:113: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:126: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:127: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:128-129: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:134: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:135: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:136-138: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:139-140: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:141-142: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:161-164: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:165-168: Lost braces in \itemize; meant \describe ? checkRd: (-1) extract_matrix.Rd:169-172: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:44-47: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:48-50: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:51-53: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:54-56: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:57-60: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:61-66: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:79: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:80-81: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:82: Lost braces 82 | \item{code{list} : \cr}{A \code{list} or character \code{vector}.} | ^ checkRd: (-1) filter_nonorthologs.Rd:82: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:95: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:96: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:97-98: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:103: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:104: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:105-107: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:108-109: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:110-111: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:147-150: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:151-154: Lost braces in \itemize; meant \describe ? checkRd: (-1) filter_nonorthologs.Rd:155-158: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:74-77: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:78-80: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:81-83: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:84-86: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:87-90: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:91-96: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:131: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:132-133: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:134: Lost braces 134 | \item{code{list} : \cr}{A \code{list} or character \code{vector}.} | ^ checkRd: (-1) generate_celltype_data.Rd:134: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:147: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:148: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:149-150: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:155: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:156: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:157-159: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:160-161: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:162-163: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:182-185: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:186-189: Lost braces in \itemize; meant \describe ? checkRd: (-1) generate_celltype_data.Rd:190-193: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:49-52: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:53-55: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:56-58: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:59-61: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:62-65: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:66-71: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:120: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:121-122: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:123: Lost braces 123 | \item{code{list} : \cr}{A \code{list} or character \code{vector}.} | ^ checkRd: (-1) standardise_ctd.Rd:123: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:136: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:137: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:138-139: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:144: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:145: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:146-148: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:149-150: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:151-152: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:171-174: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:175-178: Lost braces in \itemize; meant \describe ? checkRd: (-1) standardise_ctd.Rd:179-182: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... NOTE Documented arguments not in \usage in Rd file 'get_exp_data_for_bootstrapped_genes.Rd': 'full_results' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed controlled_geneset_enrichment 28.15 2.59 31.26 merged_ewce 22.46 1.87 29.25 generate_bootstrap_plots_for_transcriptome 18.06 1.09 19.48 filter_nonorthologs 17.50 0.66 18.44 filter_genes_without_1to1_homolog 17.12 0.65 17.84 ewce_expression_data 15.48 0.96 16.68 generate_bootstrap_plots 14.28 1.07 15.56 bootstrap_enrichment_test 13.17 1.21 14.83 add_res_to_merging_list 10.46 3.27 41.03 check_ewce_genelist_inputs 12.63 1.01 14.11 sct_normalize 11.36 0.77 13.92 filter_ctd_genes 9.38 0.83 10.66 merge_ctd 8.66 0.91 9.64 standardise_ctd 8.39 0.59 9.04 fix_bad_mgi_symbols 6.33 0.71 7.36 merge_sce 5.57 0.45 6.99 bin_specificity_into_quantiles 5.39 0.34 5.90 drop_uninformative_genes 4.86 0.56 5.79 bin_columns_into_quantiles 5.04 0.33 5.45 generate_celltype_data 4.91 0.45 5.52 plot_ctd 4.39 0.28 5.73 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/EWCE.Rcheck/00check.log' for details.
EWCE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL EWCE ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'EWCE' ... ** using staged installation ** R ** 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 (EWCE)
EWCE.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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. > library(testthat) > library(EWCE) Loading required package: RNOmni > > test_check("EWCE") 1 core(s) assigned as workers (31 reserved). Converting to sparse matrix. + Calculating normalized mean expression. Converting to sparse matrix. Converting to sparse matrix. Converting to sparse matrix. Converting to sparse matrix. + Calculating normalized specificity. Converting to sparse matrix. Converting to sparse matrix. Converting to sparse matrix. Converting to sparse matrix. Converting to sparse matrix. Converting to sparse matrix. Converting to sparse matrix. Converting to sparse matrix. Loading required namespace: ggdendro + Saving results ==> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/ctd_testthat.rda 1 core(s) assigned as workers (31 reserved). Converting to sparse matrix. + Calculating normalized mean expression. Converting to sparse matrix. Converting to sparse matrix. Converting to sparse matrix. Converting to sparse matrix. + Calculating normalized specificity. Converting to sparse matrix. Converting to sparse matrix. Converting to sparse matrix. Converting to sparse matrix. Converting to sparse matrix. Converting to sparse matrix. Converting to sparse matrix. Converting to sparse matrix. + Saving results ==> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/ctd_testthat.rda see ?ewceData and browseVignettes('ewceData') for documentation loading from cache 1 core(s) assigned as workers (31 reserved). === START walking on horizontal strip 1/5 === | processing <4159 x 3005> block from grid position [[1/5, 1/1]] ... ok === DONE walking on horizontal strip 1/5 === --- START finalizing result for horizonal strip 1/5 --- | result is a <4159 x 7> matrix --> returning as-is --- DONE finalizing result for horizonal strip 1/5 --- === START walking on horizontal strip 2/5 === | processing <4159 x 3005> block from grid position [[2/5, 1/1]] ... ok === DONE walking on horizontal strip 2/5 === --- START finalizing result for horizonal strip 2/5 --- | result is a <4159 x 7> matrix --> returning as-is --- DONE finalizing result for horizonal strip 2/5 --- === START walking on horizontal strip 3/5 === | processing <4159 x 3005> block from grid position [[3/5, 1/1]] ... ok === DONE walking on horizontal strip 3/5 === --- START finalizing result for horizonal strip 3/5 --- | result is a <4159 x 7> matrix --> returning as-is --- DONE finalizing result for horizonal strip 3/5 --- === START walking on horizontal strip 4/5 === | processing <4159 x 3005> block from grid position [[4/5, 1/1]] ... ok === DONE walking on horizontal strip 4/5 === --- START finalizing result for horizonal strip 4/5 --- | result is a <4159 x 7> matrix --> returning as-is --- DONE finalizing result for horizonal strip 4/5 --- === START walking on horizontal strip 5/5 === | processing <3336 x 3005> block from grid position [[5/5, 1/1]] ... ok === DONE walking on horizontal strip 5/5 === --- START finalizing result for horizonal strip 5/5 --- | result is a <3336 x 7> matrix --> returning as-is --- DONE finalizing result for horizonal strip 5/5 --- === FINAL STEP === | rbind()'ing strip results (5 matrices) together ... ok === DONE === Converting to sparse matrix. Converting to sparse matrix. 1 core(s) assigned as workers (31 reserved). === START walking on vertical strip 1/1 === | processing <4159 x 3005> block from grid position [[1/5, 1/1]] ... ok | processing <4159 x 3005> block from grid position [[2/5, 1/1]] ... ok | processing <4159 x 3005> block from grid position [[3/5, 1/1]] ... ok | processing <4159 x 3005> block from grid position [[4/5, 1/1]] ... ok | processing <3336 x 3005> block from grid position [[5/5, 1/1]] ... ok === DONE walking on vertical strip 1/1 === === START walking on vertical strip 1/1 === | processing <4159 x 3005> block from grid position [[1/5, 1/1]] ... ok | processing <4159 x 3005> block from grid position [[2/5, 1/1]] ... ok | processing <4159 x 3005> block from grid position [[3/5, 1/1]] ... ok | processing <4159 x 3005> block from grid position [[4/5, 1/1]] ... ok | processing <3336 x 3005> block from grid position [[5/5, 1/1]] ... ok === DONE walking on vertical strip 1/1 === Loading required namespace: sctransform Converting to sparse matrix. Calculating cell attributes from input UMI matrix: log_umi Variance stabilizing transformation of count matrix of size 17757 by 3005 Model formula is y ~ log_umi Get Negative Binomial regression parameters per gene Using 2000 genes, 3005 cells | | | 0% | |================== | 25% | |=================================== | 50% | |==================================================== | 75% | |======================================================================| 100% Found 10 outliers - those will be ignored in fitting/regularization step Second step: Get residuals using fitted parameters for 17757 genes | | | 0% | |== | 3% | |==== | 6% | |====== | 8% | |======== | 11% | |========== | 14% | |============ | 17% | |============== | 19% | |================ | 22% | |================== | 25% | |=================== | 28% | |===================== | 31% | |======================= | 33% | |========================= | 36% | |=========================== | 39% | |============================= | 42% | |=============================== | 44% | |================================= | 47% | |=================================== | 50% | |===================================== | 53% | |======================================= | 56% | |========================================= | 58% | |=========================================== | 61% | |============================================= | 64% | |=============================================== | 67% | |================================================= | 69% | |=================================================== | 72% | |==================================================== | 75% | |====================================================== | 78% | |======================================================== | 81% | |========================================================== | 83% | |============================================================ | 86% | |============================================================== | 89% | |================================================================ | 92% | |================================================================== | 94% | |==================================================================== | 97% | |======================================================================| 100% Calculating gene attributes Wall clock passed: Time difference of 50.73855 secs Computing corrected UMI count matrix | | | 0% | |== | 3% | |==== | 6% | |====== | 8% | |======== | 11% | |========== | 14% | |============ | 17% | |============== | 19% | |================ | 22% | |================== | 25% | |=================== | 28% | |===================== | 31% | |======================= | 33% | |========================= | 36% | |=========================== | 39% | |============================= | 42% | |=============================== | 44% | |================================= | 47% | |=================================== | 50% | |===================================== | 53% | |======================================= | 56% | |========================================= | 58% | |=========================================== | 61% | |============================================= | 64% | |=============================================== | 67% | |================================================= | 69% | |=================================================== | 72% | |==================================================== | 75% | |====================================================== | 78% | |======================================================== | 81% | |========================================================== | 83% | |============================================================ | 86% | |============================================================== | 89% | |================================================================ | 92% | |================================================================== | 94% | |==================================================================== | 97% | |======================================================================| 100% see ?ewceData and browseVignettes('ewceData') for documentation loading from cache + <2 non-zero quantile bins detected in column. Assigning these values to default quantile ( 20 ) see ?ewceData and browseVignettes('ewceData') for documentation loading from cache see ?ewceData and browseVignettes('ewceData') for documentation loading from cache see ?ewceData and browseVignettes('ewceData') for documentation loading from cache 1 core(s) assigned as workers (31 reserved). Generating gene background for mouse x human ==> human Gathering ortholog reports. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- mouse Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Gene table with 21,207 rows retrieved. Returning all 21,207 genes from mouse. -- -- Preparing gene_df. data.frame format detected. Extracting genes from Gene.Symbol. 21,207 genes extracted. Converting mouse ==> human orthologs using: homologene Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Checking for genes without orthologs in human. Extracting genes from input_gene. 17,355 genes extracted. Extracting genes from ortholog_gene. 17,355 genes extracted. Checking for genes without 1:1 orthologs. Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many). Filtering gene_df with gene_map Adding input_gene col to gene_df. Adding ortholog_gene col to gene_df. =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 4,725 / 21,207 (22%) Total genes remaining after convert_orthologs : 16,482 / 21,207 (78%) -- =========== REPORT SUMMARY =========== 16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion. 16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion. Gathering ortholog reports. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- human Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- =========== REPORT SUMMARY =========== 19,129 / 19,129 (100%) target_species genes remain after ortholog conversion. 19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion. 16,482 intersect background genes used. Standardising CellTypeDataset Checking gene list inputs. Running without gene size control. 17 hit gene(s) remain after filtering. Computing gene scores. Using previously sampled genes. Computing gene counts. Testing for enrichment in 7 cell types... Sorting results by p-value. Computing BH-corrected q-values. 2 significant cell type enrichment results @ q<0.05 : CellType annotLevel p fold_change sd_from_mean q 1 microglia 1 0 1.820518 2.409647 0 2 astrocytes_ependymal 1 0 1.357308 1.995351 0 Warning: sctSpecies_origin not provided. Setting to "mouse" by default. Generating gene background for mouse x human ==> human Gathering ortholog reports. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- mouse Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Gene table with 21,207 rows retrieved. Returning all 21,207 genes from mouse. -- -- Preparing gene_df. data.frame format detected. Extracting genes from Gene.Symbol. 21,207 genes extracted. Converting mouse ==> human orthologs using: homologene Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Checking for genes without orthologs in human. Extracting genes from input_gene. 17,355 genes extracted. Extracting genes from ortholog_gene. 17,355 genes extracted. Checking for genes without 1:1 orthologs. Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many). Filtering gene_df with gene_map Adding input_gene col to gene_df. Adding ortholog_gene col to gene_df. =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 4,725 / 21,207 (22%) Total genes remaining after convert_orthologs : 16,482 / 21,207 (78%) -- =========== REPORT SUMMARY =========== 16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion. 16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion. Gathering ortholog reports. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- human Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- =========== REPORT SUMMARY =========== 19,129 / 19,129 (100%) target_species genes remain after ortholog conversion. 19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion. 16,482 intersect background genes used. Standardising sct_data. Aligning celltype names with standardise_ctd format. Checking gene list inputs. 2 celltype(s) remain @ <= 0.05 Resampling random genes. Generating bootstrap plot for 2 celltype(s). Saving plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_noText____VignetteGraphs.pdf Saving plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtgene____VignetteGraphs.pdf Saving plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/bootDists____VignetteGraphs.pdf Saving plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/bootDists_LOG____VignetteGraphs.pdf $plot1 $plot2 $plot3 $plot4 Warning: genelistSpecies not provided. Setting to 'human' by default. Warning: sctSpecies_origin not provided. Setting to "mouse" by default. Warning: sctSpecies_origin not provided. Setting to "mouse" by default. Preparing gene_df. character format detected. Converting to data.frame Extracting genes from input_gene. 15,259 genes extracted. Converting mouse ==> human orthologs using: homologene Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Checking for genes without orthologs in human. Extracting genes from input_gene. 13,416 genes extracted. Extracting genes from ortholog_gene. 13,416 genes extracted. Checking for genes without 1:1 orthologs. Dropping 46 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 56 genes that have multiple ortholog_gene per input_gene (1:many). Filtering gene_df with gene_map Returning gene_map as dictionary =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 2,016 / 15,259 (13%) Total genes remaining after convert_orthologs : 13,243 / 15,259 (87%) Generating gene background for mouse x human ==> human Gathering ortholog reports. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- mouse Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Gene table with 21,207 rows retrieved. Returning all 21,207 genes from mouse. -- -- Preparing gene_df. data.frame format detected. Extracting genes from Gene.Symbol. 21,207 genes extracted. Converting mouse ==> human orthologs using: homologene Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Checking for genes without orthologs in human. Extracting genes from input_gene. 17,355 genes extracted. Extracting genes from ortholog_gene. 17,355 genes extracted. Checking for genes without 1:1 orthologs. Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many). Filtering gene_df with gene_map Adding input_gene col to gene_df. Adding ortholog_gene col to gene_df. =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 4,725 / 21,207 (22%) Total genes remaining after convert_orthologs : 16,482 / 21,207 (78%) -- =========== REPORT SUMMARY =========== 16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion. 16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion. Gathering ortholog reports. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- human Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- =========== REPORT SUMMARY =========== 19,129 / 19,129 (100%) target_species genes remain after ortholog conversion. 19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion. 16,482 intersect background genes used. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. Returning 19,129 unique genes from entire human genome. Using intersect between background gene lists: 16,482 genes. Standardising sct_data. Using 1st column of tt as gene column: HGNC.symbol 1 core(s) assigned as workers (31 reserved). Standardising CellTypeDataset Checking gene list inputs. Running without gene size control. 6 hit gene(s) remain after filtering. Computing gene scores. Using previously sampled genes. Computing gene counts. Testing for enrichment in 7 cell types... Sorting results by p-value. Computing BH-corrected q-values. 1 significant cell type enrichment results @ q<0.05 : CellType annotLevel p fold_change sd_from_mean q 1 endothelial_mural 1 0 1.960864 4.367242 0 1 core(s) assigned as workers (31 reserved). Standardising CellTypeDataset Checking gene list inputs. Running without gene size control. 5 hit gene(s) remain after filtering. Computing gene scores. Using previously sampled genes. Computing gene counts. Testing for enrichment in 7 cell types... Sorting results by p-value. Computing BH-corrected q-values. 2 significant cell type enrichment results @ q<0.05 : CellType annotLevel p fold_change sd_from_mean q 1 interneurons 1 0 1.742023 3.948853 0 2 pyramidal_SS 1 0 1.991393 3.203248 0 Warning: genelistSpecies not provided. Setting to 'human' by default. Warning: sctSpecies_origin not provided. Setting to "mouse" by default. Warning: sctSpecies_origin not provided. Setting to "mouse" by default. Aligning celltype names with standardise_ctd format. Preparing gene_df. character format detected. Converting to data.frame Extracting genes from input_gene. 15,259 genes extracted. Converting mouse ==> human orthologs using: homologene Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Checking for genes without orthologs in human. Extracting genes from input_gene. 13,416 genes extracted. Extracting genes from ortholog_gene. 13,416 genes extracted. Checking for genes without 1:1 orthologs. Dropping 46 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 56 genes that have multiple ortholog_gene per input_gene (1:many). Filtering gene_df with gene_map Returning gene_map as dictionary =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 2,016 / 15,259 (13%) Total genes remaining after convert_orthologs : 13,243 / 15,259 (87%) Generating gene background for mouse x human ==> human Gathering ortholog reports. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- mouse Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Gene table with 21,207 rows retrieved. Returning all 21,207 genes from mouse. -- -- Preparing gene_df. data.frame format detected. Extracting genes from Gene.Symbol. 21,207 genes extracted. Converting mouse ==> human orthologs using: homologene Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Checking for genes without orthologs in human. Extracting genes from input_gene. 17,355 genes extracted. Extracting genes from ortholog_gene. 17,355 genes extracted. Checking for genes without 1:1 orthologs. Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many). Filtering gene_df with gene_map Adding input_gene col to gene_df. Adding ortholog_gene col to gene_df. =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 4,725 / 21,207 (22%) Total genes remaining after convert_orthologs : 16,482 / 21,207 (78%) -- =========== REPORT SUMMARY =========== 16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion. 16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion. Gathering ortholog reports. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- human Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- =========== REPORT SUMMARY =========== 19,129 / 19,129 (100%) target_species genes remain after ortholog conversion. 19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion. 16,482 intersect background genes used. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. Returning 19,129 unique genes from entire human genome. Using intersect between background gene lists: 16,482 genes. Standardising sct_data. Using 1st column of tt as gene column: HGNC.symbol Generating exp data for bootstrap genes. Converting data for bootstrap tests to sparse matrices. endothelial_mural : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____endothelial_mural.pdf endothelial_mural : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____endothelial_mural.pdf endothelial_mural : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____endothelial_mural.pdf $plot1 $plot2 microglia : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____microglia.pdf microglia : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____microglia.pdf microglia : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____microglia.pdf $plot1 $plot2 oligodendrocytes : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____oligodendrocytes.pdf oligodendrocytes : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____oligodendrocytes.pdf oligodendrocytes : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____oligodendrocytes.pdf $plot1 $plot2 interneurons : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____interneurons.pdf interneurons : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____interneurons.pdf interneurons : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____interneurons.pdf $plot1 $plot2 astrocytes_ependymal : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____astrocytes_ependymal.pdf astrocytes_ependymal : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____astrocytes_ependymal.pdf astrocytes_ependymal : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____astrocytes_ependymal.pdf $plot1 $plot2 pyramidal_CA1 : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____pyramidal_CA1.pdf pyramidal_CA1 : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____pyramidal_CA1.pdf pyramidal_CA1 : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____pyramidal_CA1.pdf $plot1 $plot2 pyramidal_SS : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____pyramidal_SS.pdf pyramidal_SS : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____pyramidal_SS.pdf pyramidal_SS : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____pyramidal_SS.pdf $plot1 $plot2 Generating exp data for bootstrap genes. Converting data for bootstrap tests to sparse matrices. interneurons : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____interneurons.pdf interneurons : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____interneurons.pdf interneurons : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____interneurons.pdf $plot1 $plot2 pyramidal_SS : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____pyramidal_SS.pdf pyramidal_SS : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____pyramidal_SS.pdf pyramidal_SS : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____pyramidal_SS.pdf $plot1 $plot2 pyramidal_CA1 : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____pyramidal_CA1.pdf pyramidal_CA1 : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____pyramidal_CA1.pdf pyramidal_CA1 : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____pyramidal_CA1.pdf $plot1 $plot2 oligodendrocytes : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____oligodendrocytes.pdf oligodendrocytes : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____oligodendrocytes.pdf oligodendrocytes : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____oligodendrocytes.pdf $plot1 $plot2 microglia : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____microglia.pdf microglia : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____microglia.pdf microglia : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____microglia.pdf $plot1 $plot2 endothelial_mural : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____endothelial_mural.pdf endothelial_mural : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____endothelial_mural.pdf endothelial_mural : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____endothelial_mural.pdf $plot1 $plot2 astrocytes_ependymal : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____astrocytes_ependymal.pdf astrocytes_ependymal : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____astrocytes_ependymal.pdf astrocytes_ependymal : Saving bootstrap plot --> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____astrocytes_ependymal.pdf $plot1 $plot2 see ?ewceData and browseVignettes('ewceData') for documentation loading from cache see ?ewceData and browseVignettes('ewceData') for documentation loading from cache see ?ewceData and browseVignettes('ewceData') for documentation loading from cache see ?ewceData and browseVignettes('ewceData') for documentation loading from cache Preparing gene_df. character format detected. Converting to data.frame Extracting genes from input_gene. 22 genes extracted. Converting human ==> mouse orthologs using: homologene Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Checking for genes without orthologs in mouse. Extracting genes from input_gene. 17 genes extracted. Extracting genes from ortholog_gene. 17 genes extracted. Checking for genes without 1:1 orthologs. Filtering gene_df with gene_map Returning gene_map as dictionary =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 5 / 22 (23%) Total genes remaining after convert_orthologs : 17 / 22 (77%) 1 core(s) assigned as workers (31 reserved). 1 core(s) assigned as workers (31 reserved). Generating gene background for mouse x human ==> human Gathering ortholog reports. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- mouse Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Gene table with 21,207 rows retrieved. Returning all 21,207 genes from mouse. -- -- Preparing gene_df. data.frame format detected. Extracting genes from Gene.Symbol. 21,207 genes extracted. Converting mouse ==> human orthologs using: homologene Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Checking for genes without orthologs in human. Extracting genes from input_gene. 17,355 genes extracted. Extracting genes from ortholog_gene. 17,355 genes extracted. Checking for genes without 1:1 orthologs. Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many). Filtering gene_df with gene_map Adding input_gene col to gene_df. Adding ortholog_gene col to gene_df. =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 4,725 / 21,207 (22%) Total genes remaining after convert_orthologs : 16,482 / 21,207 (78%) -- =========== REPORT SUMMARY =========== 16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion. 16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion. Gathering ortholog reports. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- human Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- =========== REPORT SUMMARY =========== 19,129 / 19,129 (100%) target_species genes remain after ortholog conversion. 19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion. 16,482 intersect background genes used. Standardising CellTypeDataset Checking gene list inputs. Running with gene size control. Warning: sctSpecies_origin not provided. Setting to "mouse" by default. Retrieving all genes using: gprofiler Retrieving all organisms available in gprofiler. Using stored `gprofiler_orgs`. Mapping species name: human Common name mapping found for human 1 organism identified from search: hsapiens Gene table with 63,150 rows retrieved. Returning all 63,150 genes from human. 63,150 human Ensembl IDs and 40,977 human Gene Symbols imported. see ?ewceData and browseVignettes('ewceData') for documentation loading from cache Controlled bootstrapping network generated. 17 hit gene(s) remain after filtering. Computing gene scores. Using previously sampled genes. Computing gene counts. Testing for enrichment in 7 cell types... Sorting results by p-value. Computing BH-corrected q-values. 1 significant cell type enrichment results @ q<0.05 : CellType annotLevel p fold_change sd_from_mean q 1 microglia 1 0 2.079331 5.793469 0 1 core(s) assigned as workers (31 reserved). Returning 15,604 unique genes from the user-supplied bg. Standardising CellTypeDataset Checking gene list inputs. Converting gene list input to standardised human genes. 1 core(s) assigned as workers (31 reserved). Returning 15,589 unique genes from the user-supplied bg. Standardising CellTypeDataset Checking gene list inputs. Converting gene list input to standardised human genes. Preparing gene_df. character format detected. Converting to data.frame Extracting genes from input_gene. 22 genes extracted. Converting human ==> rat orthologs using: homologene Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Retrieving all organisms available in homologene. Mapping species name: rat Common name mapping found for rat 1 organism identified from search: 10116 Checking for genes without orthologs in rat. Extracting genes from input_gene. 18 genes extracted. Extracting genes from ortholog_gene. 18 genes extracted. Checking for genes without 1:1 orthologs. Dropping 2 genes that have multiple input_gene per ortholog_gene (many:1). Filtering gene_df with gene_map Returning gene_map as dictionary =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 7 / 22 (32%) Total genes remaining after convert_orthologs : 15 / 22 (68%) 1 core(s) assigned as workers (31 reserved). Generating gene background for mouse x rat ==> human Gathering ortholog reports. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- mouse Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Gene table with 21,207 rows retrieved. Returning all 21,207 genes from mouse. -- -- Preparing gene_df. data.frame format detected. Extracting genes from Gene.Symbol. 21,207 genes extracted. Converting mouse ==> human orthologs using: homologene Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Checking for genes without orthologs in human. Extracting genes from input_gene. 17,355 genes extracted. Extracting genes from ortholog_gene. 17,355 genes extracted. Checking for genes without 1:1 orthologs. Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many). Filtering gene_df with gene_map Adding input_gene col to gene_df. Adding ortholog_gene col to gene_df. =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 4,725 / 21,207 (22%) Total genes remaining after convert_orthologs : 16,482 / 21,207 (78%) -- =========== REPORT SUMMARY =========== 16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion. 16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion. Gathering ortholog reports. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- rat Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: rat Common name mapping found for rat 1 organism identified from search: 10116 Gene table with 20,616 rows retrieved. Returning all 20,616 genes from rat. -- -- Preparing gene_df. data.frame format detected. Extracting genes from Gene.Symbol. 20,616 genes extracted. Converting rat ==> human orthologs using: homologene Retrieving all organisms available in homologene. Mapping species name: rat Common name mapping found for rat 1 organism identified from search: 10116 Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Checking for genes without orthologs in human. Extracting genes from input_gene. 16,989 genes extracted. Extracting genes from ortholog_gene. 16,989 genes extracted. Checking for genes without 1:1 orthologs. Dropping 122 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 607 genes that have multiple ortholog_gene per input_gene (1:many). Filtering gene_df with gene_map Adding input_gene col to gene_df. Adding ortholog_gene col to gene_df. =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 4,813 / 20,616 (23%) Total genes remaining after convert_orthologs : 15,803 / 20,616 (77%) -- =========== REPORT SUMMARY =========== 15,803 / 20,616 (76.65%) target_species genes remain after ortholog conversion. 15,803 / 19,129 (82.61%) reference_species genes remain after ortholog conversion. 15,450 intersect background genes used. Standardising CellTypeDataset Checking gene list inputs. Converting gene list input to standardised human genes. Running without gene size control. 15 hit gene(s) remain after filtering. Computing gene scores. Using previously sampled genes. Computing gene counts. Testing for enrichment in 7 cell types... Sorting results by p-value. Computing BH-corrected q-values. 1 significant cell type enrichment results @ q<0.05 : CellType annotLevel p fold_change sd_from_mean q 1 microglia 1 0 2.156018 4.415353 0 Standardising CellTypeDataset Found 5 matrix types across 2 CTD levels. Processing level: 1 Processing level: 2 1 core(s) assigned as workers (31 reserved). failed to open the port 11228, trying a new port... Generating gene background for monkey x mouse ==> human Gathering ortholog reports. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- monkey Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: monkey Common name mapping found for monkey 1 organism identified from search: 9544 Gene table with 16,843 rows retrieved. Returning all 16,843 genes from monkey. -- -- Preparing gene_df. data.frame format detected. Extracting genes from Gene.Symbol. 16,843 genes extracted. Converting monkey ==> human orthologs using: homologene Retrieving all organisms available in homologene. Mapping species name: monkey Common name mapping found for monkey 1 organism identified from search: 9544 Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Checking for genes without orthologs in human. Extracting genes from input_gene. 15,675 genes extracted. Extracting genes from ortholog_gene. 15,675 genes extracted. Checking for genes without 1:1 orthologs. Dropping 197 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 215 genes that have multiple ortholog_gene per input_gene (1:many). Filtering gene_df with gene_map Adding input_gene col to gene_df. Adding ortholog_gene col to gene_df. =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 1,726 / 16,816 (10%) Total genes remaining after convert_orthologs : 15,090 / 16,816 (90%) -- =========== REPORT SUMMARY =========== 15,077 / 16,816 (89.66%) target_species genes remain after ortholog conversion. 15,077 / 19,129 (78.82%) reference_species genes remain after ortholog conversion. Gathering ortholog reports. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- mouse Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Gene table with 21,207 rows retrieved. Returning all 21,207 genes from mouse. -- -- Preparing gene_df. data.frame format detected. Extracting genes from Gene.Symbol. 21,207 genes extracted. Converting mouse ==> human orthologs using: homologene Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Checking for genes without orthologs in human. Extracting genes from input_gene. 17,355 genes extracted. Extracting genes from ortholog_gene. 17,355 genes extracted. Checking for genes without 1:1 orthologs. Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many). Filtering gene_df with gene_map Adding input_gene col to gene_df. Adding ortholog_gene col to gene_df. =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 4,725 / 21,207 (22%) Total genes remaining after convert_orthologs : 16,482 / 21,207 (78%) -- =========== REPORT SUMMARY =========== 16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion. 16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion. 13,875 intersect background genes used. Standardising CellTypeDataset Checking gene list inputs. Converting gene list input to standardised human genes. Running without gene size control. 11 hit gene(s) remain after filtering. Testing for enrichment in 7 cell types... Sorting results by p-value. Computing BH-corrected q-values. 0 significant cell type enrichment results @ q<0.05 : 1 core(s) assigned as workers (31 reserved). Generating gene background for godzilla x mouse ==> human Gathering ortholog reports. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- godzilla 1 core(s) assigned as workers (31 reserved). Generating gene background for mouse x human ==> human Gathering ortholog reports. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- mouse Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Gene table with 21,207 rows retrieved. Returning all 21,207 genes from mouse. -- -- Preparing gene_df. data.frame format detected. Extracting genes from Gene.Symbol. 21,207 genes extracted. Converting mouse ==> human orthologs using: homologene Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Checking for genes without orthologs in human. Extracting genes from input_gene. 17,355 genes extracted. Extracting genes from ortholog_gene. 17,355 genes extracted. Checking for genes without 1:1 orthologs. Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many). Filtering gene_df with gene_map Adding input_gene col to gene_df. Adding ortholog_gene col to gene_df. =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 4,725 / 21,207 (22%) Total genes remaining after convert_orthologs : 16,482 / 21,207 (78%) -- =========== REPORT SUMMARY =========== 16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion. 16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion. Gathering ortholog reports. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- human Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- =========== REPORT SUMMARY =========== 19,129 / 19,129 (100%) target_species genes remain after ortholog conversion. 19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion. 16,482 intersect background genes used. Standardising CellTypeDataset Checking gene list inputs. 1 core(s) assigned as workers (31 reserved). Returning 15,604 unique genes from the user-supplied bg. Standardising CellTypeDataset Checking gene list inputs. see ?ewceData and browseVignettes('ewceData') for documentation loading from cache Check 1000Check 3005 Warning: sctSpecies not provided. Setting to 'mouse' by default. Warning: sctSpecies_origin not provided. Setting to "mouse" by default. 1 core(s) assigned as workers (31 reserved). Converting to sparse matrix. Checking for non-expressed genes. Checking for cells with no expressed genes. DGE:: Limma... 248 / 1,000 genes dropped @ DGE adj_pval_thresh < 1e-05 Time difference of 0.818619 secs 1 core(s) assigned as workers (31 reserved). Converting to sparse matrix. + Calculating normalized mean expression. Converting to sparse matrix. Converting to sparse matrix. + Calculating normalized specificity. Converting to sparse matrix. Converting to sparse matrix. Converting to sparse matrix. Converting to sparse matrix. + Saving results ==> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/ctd_kiCortexOnly.rda 1 core(s) assigned as workers (31 reserved). Converting to sparse matrix. + Calculating normalized mean expression. Converting to sparse matrix. Converting to sparse matrix. + Calculating normalized specificity. Converting to sparse matrix. Converting to sparse matrix. Converting to sparse matrix. Converting to sparse matrix. Converting to sparse matrix. Converting to sparse matrix. + Saving results ==> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/ctd_kiCortexOnly.rda Loading precomputed example bootstrap results. Aligning celltype names with standardise_ctd format. 7 signficiant enrichment results @ bonferroni < 0.05 14.3% of hits are of the target cell type. see ?ewceData and browseVignettes('ewceData') for documentation loading from cache see ?ewceData and browseVignettes('ewceData') for documentation loading from cache see ?ewceData and browseVignettes('ewceData') for documentation loading from cache see ?ewceData and browseVignettes('ewceData') for documentation loading from cache Warning: sctSpecies_origin not provided. Setting to "mouse" by default. Warning: sctSpecies_origin not provided. Setting to "mouse" by default. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Gene table with 21,207 rows retrieved. Returning all 21,207 genes from mouse. Standardising CellTypeDataset Found 5 matrix types across 2 CTD levels. Processing level: 1 Processing level: 2 Generating controlled bootstrap gene sets. see ?ewceData and browseVignettes('ewceData') for documentation loading from cache see ?ewceData and browseVignettes('ewceData') for documentation loading from cache Warning: genelistSpecies not provided. Setting to 'human' by default. Warning: sctSpecies_origin not provided. Setting to "mouse" by default. Warning: sctSpecies_origin not provided. Setting to "mouse" by default. Preparing gene_df. character format detected. Converting to data.frame Extracting genes from input_gene. 15,259 genes extracted. Converting mouse ==> human orthologs using: homologene Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Checking for genes without orthologs in human. Extracting genes from input_gene. 13,416 genes extracted. Extracting genes from ortholog_gene. 13,416 genes extracted. Checking for genes without 1:1 orthologs. Dropping 46 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 56 genes that have multiple ortholog_gene per input_gene (1:many). Filtering gene_df with gene_map Returning gene_map as dictionary =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 2,016 / 15,259 (13%) Total genes remaining after convert_orthologs : 13,243 / 15,259 (87%) Generating gene background for mouse x human ==> human Gathering ortholog reports. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- mouse Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Gene table with 21,207 rows retrieved. Returning all 21,207 genes from mouse. -- -- Preparing gene_df. data.frame format detected. Extracting genes from Gene.Symbol. 21,207 genes extracted. Converting mouse ==> human orthologs using: homologene Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Checking for genes without orthologs in human. Extracting genes from input_gene. 17,355 genes extracted. Extracting genes from ortholog_gene. 17,355 genes extracted. Checking for genes without 1:1 orthologs. Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many). Filtering gene_df with gene_map Adding input_gene col to gene_df. Adding ortholog_gene col to gene_df. =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 4,725 / 21,207 (22%) Total genes remaining after convert_orthologs : 16,482 / 21,207 (78%) -- =========== REPORT SUMMARY =========== 16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion. 16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion. Gathering ortholog reports. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- human Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- =========== REPORT SUMMARY =========== 19,129 / 19,129 (100%) target_species genes remain after ortholog conversion. 19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion. 16,482 intersect background genes used. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. Returning 19,129 unique genes from entire human genome. Using intersect between background gene lists: 16,482 genes. Standardising sct_data. Using 1st column of tt as gene column: HGNC.symbol 1 core(s) assigned as workers (31 reserved). Standardising CellTypeDataset Checking gene list inputs. Running without gene size control. 28 hit gene(s) remain after filtering. Computing gene scores. Using previously sampled genes. Computing gene counts. Testing for enrichment in 7 cell types... Sorting results by p-value. Computing BH-corrected q-values. 1 significant cell type enrichment results @ q<0.05 : CellType annotLevel p fold_change sd_from_mean q 1 endothelial_mural 1 0 1.628635 4.684982 0 1 core(s) assigned as workers (31 reserved). Standardising CellTypeDataset Checking gene list inputs. Running without gene size control. 26 hit gene(s) remain after filtering. Computing gene scores. Using previously sampled genes. Computing gene counts. Testing for enrichment in 7 cell types... Sorting results by p-value. Computing BH-corrected q-values. 0 significant cell type enrichment results @ q<0.05 : see ?ewceData and browseVignettes('ewceData') for documentation loading from cache see ?ewceData and browseVignettes('ewceData') for documentation loading from cache Warning: genelistSpecies not provided. Setting to 'human' by default. Warning: sctSpecies_origin not provided. Setting to "mouse" by default. Warning: sctSpecies_origin not provided. Setting to "mouse" by default. Preparing gene_df. character format detected. Converting to data.frame Extracting genes from input_gene. 15,259 genes extracted. Converting mouse ==> human orthologs using: homologene Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Checking for genes without orthologs in human. Extracting genes from input_gene. 13,416 genes extracted. Extracting genes from ortholog_gene. 13,416 genes extracted. Checking for genes without 1:1 orthologs. Dropping 46 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 56 genes that have multiple ortholog_gene per input_gene (1:many). Filtering gene_df with gene_map Returning gene_map as dictionary =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 2,016 / 15,259 (13%) Total genes remaining after convert_orthologs : 13,243 / 15,259 (87%) Generating gene background for mouse x human ==> human Gathering ortholog reports. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- mouse Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Gene table with 21,207 rows retrieved. Returning all 21,207 genes from mouse. -- -- Preparing gene_df. data.frame format detected. Extracting genes from Gene.Symbol. 21,207 genes extracted. Converting mouse ==> human orthologs using: homologene Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Checking for genes without orthologs in human. Extracting genes from input_gene. 17,355 genes extracted. Extracting genes from ortholog_gene. 17,355 genes extracted. Checking for genes without 1:1 orthologs. Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many). Filtering gene_df with gene_map Adding input_gene col to gene_df. Adding ortholog_gene col to gene_df. =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 4,725 / 21,207 (22%) Total genes remaining after convert_orthologs : 16,482 / 21,207 (78%) -- =========== REPORT SUMMARY =========== 16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion. 16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion. Gathering ortholog reports. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- human Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- =========== REPORT SUMMARY =========== 19,129 / 19,129 (100%) target_species genes remain after ortholog conversion. 19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion. 16,482 intersect background genes used. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. Returning 19,129 unique genes from entire human genome. Using intersect between background gene lists: 16,482 genes. Standardising sct_data. Using 1st column of tt as gene column: HGNC.symbol 1 core(s) assigned as workers (31 reserved). Standardising CellTypeDataset Checking gene list inputs. Running without gene size control. 10 hit gene(s) remain after filtering. Computing gene scores. Using previously sampled genes. Computing gene counts. Testing for enrichment in 7 cell types... Sorting results by p-value. Computing BH-corrected q-values. 0 significant cell type enrichment results @ q<0.05 : 1 core(s) assigned as workers (31 reserved). Standardising CellTypeDataset Checking gene list inputs. Running without gene size control. 8 hit gene(s) remain after filtering. Computing gene scores. Using previously sampled genes. Computing gene counts. Testing for enrichment in 7 cell types... Sorting results by p-value. Computing BH-corrected q-values. 1 significant cell type enrichment results @ q<0.05 : CellType annotLevel p fold_change sd_from_mean q 1 pyramidal_CA1 1 0 1.318978 1.682404 0 Warning: genelistSpecies not provided. Setting to 'human' by default. Warning: sctSpecies_origin not provided. Setting to "mouse" by default. Warning: sctSpecies_origin not provided. Setting to "mouse" by default. Preparing gene_df. character format detected. Converting to data.frame Extracting genes from input_gene. 15,259 genes extracted. Converting mouse ==> human orthologs using: homologene Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Checking for genes without orthologs in human. Extracting genes from input_gene. 13,416 genes extracted. Extracting genes from ortholog_gene. 13,416 genes extracted. Checking for genes without 1:1 orthologs. Dropping 46 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 56 genes that have multiple ortholog_gene per input_gene (1:many). Filtering gene_df with gene_map Returning gene_map as dictionary =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 2,016 / 15,259 (13%) Total genes remaining after convert_orthologs : 13,243 / 15,259 (87%) Generating gene background for mouse x human ==> human Gathering ortholog reports. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- mouse Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Gene table with 21,207 rows retrieved. Returning all 21,207 genes from mouse. -- -- Preparing gene_df. data.frame format detected. Extracting genes from Gene.Symbol. 21,207 genes extracted. Converting mouse ==> human orthologs using: homologene Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Checking for genes without orthologs in human. Extracting genes from input_gene. 17,355 genes extracted. Extracting genes from ortholog_gene. 17,355 genes extracted. Checking for genes without 1:1 orthologs. Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many). Filtering gene_df with gene_map Adding input_gene col to gene_df. Adding ortholog_gene col to gene_df. =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 4,725 / 21,207 (22%) Total genes remaining after convert_orthologs : 16,482 / 21,207 (78%) -- =========== REPORT SUMMARY =========== 16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion. 16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion. Gathering ortholog reports. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- human Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. -- =========== REPORT SUMMARY =========== 19,129 / 19,129 (100%) target_species genes remain after ortholog conversion. 19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion. 16,482 intersect background genes used. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from human. Returning 19,129 unique genes from entire human genome. Using intersect between background gene lists: 16,482 genes. Standardising sct_data. Using 1st column of tt as gene column: HGNC.symbol 1 core(s) assigned as workers (31 reserved). Standardising CellTypeDataset Checking gene list inputs. Running without gene size control. 11 hit gene(s) remain after filtering. Computing gene scores. Using previously sampled genes. Computing gene counts. Testing for enrichment in 7 cell types... Sorting results by p-value. Computing BH-corrected q-values. 0 significant cell type enrichment results @ q<0.05 : 1 core(s) assigned as workers (31 reserved). Standardising CellTypeDataset Checking gene list inputs. Running without gene size control. 9 hit gene(s) remain after filtering. Computing gene scores. Using previously sampled genes. Computing gene counts. Testing for enrichment in 7 cell types... Sorting results by p-value. Computing BH-corrected q-values. 0 significant cell type enrichment results @ q<0.05 : Loading precomputed example bootstrap results. see ?ewceData and browseVignettes('ewceData') for documentation loading from cache see ?ewceData and browseVignettes('ewceData') for documentation loading from cache Filtering CTD to 100 genes. level: 1 Found 5 matrix types across 1 CTD levels. - mean_exp - median_exp - specificity - median_specificity - specificity_quantiles level: 2 Found 5 matrix types across 1 CTD levels. - mean_exp - median_exp - specificity - median_specificity - specificity_quantiles Standardising CellTypeDataset Found 5 matrix types across 2 CTD levels. Processing level: 1 Processing level: 2 Filtering CTD to 100 genes. level: level_1 Found 5 matrix types across 1 CTD levels. - mean_exp - median_exp - specificity - median_specificity - specificity_quantiles level: level_2 Found 5 matrix types across 1 CTD levels. - mean_exp - median_exp - specificity - median_specificity - specificity_quantiles see ?ewceData and browseVignettes('ewceData') for documentation loading from cache Check 1000Check 3005 Warning: sctSpecies_origin not provided. Setting to "mouse" by default. 1 core(s) assigned as workers (31 reserved). Converting to sparse matrix. Checking for non-expressed genes. Checking for cells with no expressed genes. DGE:: Limma... 248 / 1,000 genes dropped @ DGE adj_pval_thresh < 1e-05 Time difference of 0.7941101 secs 1 core(s) assigned as workers (31 reserved). Converting to sparse matrix. + Calculating normalized mean expression. Converting to sparse matrix. Converting to sparse matrix. + Calculating normalized specificity. Converting to sparse matrix. Converting to sparse matrix. Converting to sparse matrix. Converting to sparse matrix. + Saving results ==> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/ctd_kiCortexOnly.rda + Processing level 1 ... Processing mean_exp Processing specificity Processing specificity_quantiles + Processing level 2 ... Processing mean_exp Processing specificity Processing specificity_quantiles No input_species provided. Setting to 'mouse' + Processing level 1 ... Processing mean_exp Processing specificity Processing specificity_quantiles + Processing level 2 ... Processing mean_exp Processing specificity Processing specificity_quantiles see ?ewceData and browseVignettes('ewceData') for documentation loading from cache trying URL 'http://www.informatics.jax.org/downloads/reports/MRK_List2.rpt' Content type 'unknown' length 86778667 bytes (82.8 MB) ================================================== downloaded 82.8 MB see ?ewceData and browseVignettes('ewceData') for documentation loading from cache 1 rows do not have proper MGI symbols Mar-01 see ?ewceData and browseVignettes('ewceData') for documentation loading from cache 1 rows do not have proper MGI symbols Mar-01 see ?ewceData and browseVignettes('ewceData') for documentation loading from cache 10 of 10 are not proper HGNC symbols. Possible corruption of gene names by excel: Mar-01 see ?ewceData and browseVignettes('ewceData') for documentation loading from cache 10 of 10 are not proper HGNC symbols. Possible corruption of gene names by excel: Mar-01 see ?ewceData and browseVignettes('ewceData') for documentation loading from cache 10 of 10 are not proper HGNC symbols. Possible corruption of gene names by excel: Mar-01 Maps last updated on: Fri May 17 15:09:37 2024 Maps last updated on: Fri May 17 15:09:37 2024 9 of 10 gene symbols corrected. 1 of 10 gene symbols cannot be mapped. Converting to sparse matrix. see ?ewceData and browseVignettes('ewceData') for documentation loading from cache 1 rows do not have proper MGI symbols Tm4sf12 see ?ewceData and browseVignettes('ewceData') for documentation loading from cache 1 poorly annotated genes are replicates of existing genes. These are: Tspan12 Converting to sparse matrix. 1 rows should have been corrected by checking synonyms. 0 rows STILL do not have proper MGI symbols. see ?ewceData and browseVignettes('ewceData') for documentation loading from cache 0 rows do not have proper MGI symbols see ?ewceData and browseVignettes('ewceData') for documentation loading from cache 669 rows do not have proper MGI symbols 2310042E22Rik, BC005764, C130030K03Rik, Stmn1-rs1, Gm9846, E130309F12Rik, Fam211b, AI848285, Acpl2, 9630033F20Rik, Adrbk2, Syne1_loc2, Adc, Dlx1os, LOC106740, Pdxp, Atp6v0c-ps2, 2900056M20Rik, Epb4.1l1, A330050F15Rik see ?ewceData and browseVignettes('ewceData') for documentation loading from cache 308 rows do not have proper MGI symbols 2310042E22Rik, BC005764, C130030K03Rik, Stmn1-rs1, Gm9846, E130309F12Rik, Fam211b, AI848285, Acpl2, 9630033F20Rik, Adrbk2, Syne1_loc2, Adc, Dlx1os, LOC106740, Pdxp, Atp6v0c-ps2, 2900056M20Rik, Epb4.1l1, A330050F15Rik see ?ewceData and browseVignettes('ewceData') for documentation loading from cache 1 poorly annotated genes are replicates of existing genes. These are: Hjurp Converting to sparse matrix. 185 rows should have been corrected by checking synonyms. 126 rows STILL do not have proper MGI symbols. see ?ewceData and browseVignettes('ewceData') for documentation loading from cache 308 rows do not have proper MGI symbols 2310042E22Rik, BC005764, C130030K03Rik, Stmn1-rs1, Gm9846, E130309F12Rik, Fam211b, AI848285, Acpl2, 9630033F20Rik, Adrbk2, Syne1_loc2, Adc, Dlx1os, LOC106740, Pdxp, Atp6v0c-ps2, 2900056M20Rik, Epb4.1l1, A330050F15Rik see ?ewceData and browseVignettes('ewceData') for documentation loading from cache 1 poorly annotated genes are replicates of existing genes. These are: Hjurp Converting to sparse matrix. 185 rows should have been corrected by checking synonyms. 126 rows STILL do not have proper MGI symbols. see ?ewceData and browseVignettes('ewceData') for documentation loading from cache 1 core(s) assigned as workers (31 reserved). Preparing gene_df. Dense matrix format detected. Extracting genes from rownames. 100 genes extracted. Converting mouse ==> human orthologs using: homologene Retrieving all organisms available in homologene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Checking for genes without orthologs in human. Extracting genes from input_gene. 91 genes extracted. Extracting genes from ortholog_gene. 91 genes extracted. Checking for genes without 1:1 orthologs. Filtering gene_df with gene_map Setting ortholog_gene to rownames. Converting obj to sparseMatrix. =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 9 / 100 (9%) Total genes remaining after convert_orthologs : 91 / 100 (91%) Converting to sparse matrix. Converting to DelayedArray. + Calculating normalized mean expression. === START walking on horizontal strip 1/1 === | processing <91 x 3005> sparse block from grid position [[1/1, 1/1]] ... ok === DONE walking on horizontal strip 1/1 === --- START finalizing result for horizonal strip 1/1 --- | result is a <91 x 7> matrix --> returning as-is --- DONE finalizing result for horizonal strip 1/1 --- Converting to sparse matrix. === START walking on horizontal strip 1/1 === | processing <91 x 3005> sparse block from grid position [[1/1, 1/1]] ... ok === DONE walking on horizontal strip 1/1 === --- START finalizing result for horizonal strip 1/1 --- | result is a <91 x 48> matrix --> returning as-is --- DONE finalizing result for horizonal strip 1/1 --- Converting to sparse matrix. + Calculating normalized specificity. Converting to sparse matrix. Converting to sparse matrix. Converting to sparse matrix. Converting to sparse matrix. + Saving results ==> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/ctd_allKImouse.rda + Returning list of CTD file name, and the CTD itself. see ?ewceData and browseVignettes('ewceData') for documentation loading from cache Filtering by variance quantiles. Converting to DelayedArray. 120 / 300 genes dropped @ DGE min_variance_quantile >= 5 Converting to sparse matrix. Calculating cell attributes from input UMI matrix: log_umi Variance stabilizing transformation of count matrix of size 300 by 3005 Model formula is y ~ log_umi Get Negative Binomial regression parameters per gene Using 300 genes, 3005 cells | | | 0% | |======================================================================| 100% Found 2 outliers - those will be ignored in fitting/regularization step Second step: Get residuals using fitted parameters for 300 genes | | | 0% | |======================================================================| 100% Calculating gene attributes Wall clock passed: Time difference of 9.348733 secs Computing corrected UMI count matrix | | | 0% | |======================================================================| 100% Filtering by variance quantiles. Converting to DelayedArray. 120 / 300 genes dropped @ DGE min_variance_quantile >= 5 Filtering by variance quantiles. Converting to DelayedArray. 120 / 300 genes dropped @ DGE min_variance_quantile >= 5 Filtering by variance quantiles. Converting to DelayedArray. / reading and realizing block 1/1 ... ok \ processing it ... ok 120 / 300 genes dropped @ DGE min_variance_quantile >= 5 Retrieving all organisms available in homologene. Returning table with all species. see ?ewceData and browseVignettes('ewceData') for documentation loading from cache + CTD ==> SingleCellExperiment Converting level: level_1 Returning all possible matrix names. Converting level: level_2 Returning all possible matrix names. The assay 'mean_exp' will be used to determine the proportion of zeroes for each batch. Converting CTD to merged SCEs ctd1 + CTD ==> SingleCellExperiment Converting level: level_1 Returning all possible matrix names. Converting level: level_2 Returning all possible matrix names. ctd2 + CTD ==> SingleCellExperiment Converting level: level_1 Returning all possible matrix names. Converting level: level_2 Returning all possible matrix names. Merging SCE at level: 1 [1] "ctd1" [1] "15259 x 7" [1] "ctd2" [1] "15259 x 7" The assay 'mean_exp' will be used to determine the proportion of zeroes for each batch. Merging SCE at level: 2 [1] "ctd1" [1] "15259 x 48" [1] "ctd2" [1] "15259 x 48" The assay 'mean_exp' will be used to determine the proportion of zeroes for each batch. [1] "level_1" [1] "level_2" Saving SCE_merged ==> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/merged/CTD_SCE_merged.union.rds + Must set `as_SCE=TRUE` in order to merge CTD. + Returning merged CTD. 1 core(s) assigned as workers (31 reserved). Converting to sparse matrix. + Calculating normalized mean expression. Converting to sparse matrix. + Calculating normalized specificity. Converting to sparse matrix. Converting to sparse matrix. + Saving results ==> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/ctd_file16e2031c774e1level_1.rda + Returning list of CTD file name, and the CTD itself. 1 core(s) assigned as workers (31 reserved). Converting to sparse matrix. + Calculating normalized mean expression. Converting to sparse matrix. + Calculating normalized specificity. Converting to sparse matrix. Converting to sparse matrix. + Saving results ==> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpkvegMq/ctd_file16e207176157clevel_2.rda + Returning list of CTD file name, and the CTD itself. see ?ewceData and browseVignettes('ewceData') for documentation loading from cache 0 non-overlapping gene(s) removed from exp1. 0 non-overlapping gene(s) removed from exp2. 19,972 intersecting genes remain. Converting to data.frame Converting to data.frame Converting to sparse matrix. see ?ewceData and browseVignettes('ewceData') for documentation loading from cache DGE:: Limma... Loading required namespace: DESeq2 DGE:: DESeq2... 1 core(s) assigned as workers (31 reserved). converting counts to integer mode Note: levels of factors in the design contain characters other than letters, numbers, '_' and '.'. It is recommended (but not required) to use only letters, numbers, and delimiters '_' or '.', as these are safe characters for column names in R. [This is a message, not a warning or an error] estimating size factors Note: levels of factors in the design contain characters other than letters, numbers, '_' and '.'. It is recommended (but not required) to use only letters, numbers, and delimiters '_' or '.', as these are safe characters for column names in R. [This is a message, not a warning or an error] estimating dispersions gene-wise dispersion estimates mean-dispersion relationship -- note: fitType='parametric', but the dispersion trend was not well captured by the function: y = a/x + b, and a local regression fit was automatically substituted. specify fitType='local' or 'mean' to avoid this message next time. Note: levels of factors in the design contain characters other than letters, numbers, '_' and '.'. It is recommended (but not required) to use only letters, numbers, and delimiters '_' or '.', as these are safe characters for column names in R. [This is a message, not a warning or an error] final dispersion estimates fitting model and testing Note: levels of factors in the design contain characters other than letters, numbers, '_' and '.'. It is recommended (but not required) to use only letters, numbers, and delimiters '_' or '.', as these are safe characters for column names in R. [This is a message, not a warning or an error] Loading required namespace: MAST `fData` has no primerid. I'll make something up. `cData` has no wellKey. I'll make something up. [ FAIL 0 | WARN 44 | SKIP 0 | PASS 134 ] [ FAIL 0 | WARN 44 | SKIP 0 | PASS 134 ] > > proc.time() user system elapsed 534.54 39.10 611.46
EWCE.Rcheck/EWCE-Ex.timings
name | user | system | elapsed | |
add_res_to_merging_list | 10.46 | 3.27 | 41.03 | |
bin_columns_into_quantiles | 5.04 | 0.33 | 5.45 | |
bin_specificity_into_quantiles | 5.39 | 0.34 | 5.90 | |
bootstrap_enrichment_test | 13.17 | 1.21 | 14.83 | |
check_ewce_genelist_inputs | 12.63 | 1.01 | 14.11 | |
check_percent_hits | 0.00 | 0.00 | 0.02 | |
controlled_geneset_enrichment | 28.15 | 2.59 | 31.26 | |
ctd_to_sce | 4.43 | 0.40 | 4.91 | |
drop_uninformative_genes | 4.86 | 0.56 | 5.79 | |
ewce_expression_data | 15.48 | 0.96 | 16.68 | |
ewce_plot | 0.04 | 0.01 | 0.06 | |
example_bootstrap_results | 0.00 | 0.02 | 0.02 | |
example_transcriptome_results | 0.00 | 0.00 | 0.01 | |
filter_ctd_genes | 9.38 | 0.83 | 10.66 | |
filter_genes_without_1to1_homolog | 17.12 | 0.65 | 17.84 | |
filter_nonorthologs | 17.50 | 0.66 | 18.44 | |
fix_bad_hgnc_symbols | 1.38 | 0.19 | 1.78 | |
fix_bad_mgi_symbols | 6.33 | 0.71 | 7.36 | |
fix_celltype_names | 0 | 0 | 0 | |
generate_bootstrap_plots | 14.28 | 1.07 | 15.56 | |
generate_bootstrap_plots_for_transcriptome | 18.06 | 1.09 | 19.48 | |
generate_celltype_data | 4.91 | 0.45 | 5.52 | |
get_celltype_table | 3.84 | 0.47 | 4.37 | |
list_species | 0.02 | 0.00 | 0.02 | |
load_rdata | 0.00 | 0.00 | 0.03 | |
merge_ctd | 8.66 | 0.91 | 9.64 | |
merge_sce | 5.57 | 0.45 | 6.99 | |
merge_two_expfiles | 3.90 | 0.49 | 4.50 | |
merged_ewce | 22.46 | 1.87 | 29.25 | |
plot_ctd | 4.39 | 0.28 | 5.73 | |
sct_normalize | 11.36 | 0.77 | 13.92 | |
standardise_ctd | 8.39 | 0.59 | 9.04 | |