Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:41 -0400 (Wed, 21 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" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 1458/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
orthogene 1.11.0 (landing page) Brian Schilder
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
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 orthogene package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/orthogene.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: orthogene |
Version: 1.11.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:orthogene.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings orthogene_1.11.0.tar.gz |
StartedAt: 2024-08-21 03:31:08 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 03:41:01 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 593.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: orthogene.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:orthogene.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings orthogene_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/orthogene.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 'orthogene/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'orthogene' version '1.11.0' * 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 'orthogene' 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) aggregate_mapped_genes.Rd:37-40: Lost braces in \itemize; meant \describe ? checkRd: (-1) aggregate_mapped_genes.Rd:41-44: Lost braces in \itemize; meant \describe ? checkRd: (-1) aggregate_mapped_genes.Rd:45-48: Lost braces in \itemize; meant \describe ? checkRd: (-1) check_gene_df_type.Rd:15: Lost braces in \itemize; meant \describe ? checkRd: (-1) check_gene_df_type.Rd:16-17: Lost braces in \itemize; meant \describe ? checkRd: (-1) check_gene_df_type.Rd:18: Lost braces 18 | \item{code{list} : \cr}{A \code{list} or character \code{vector}.} | ^ checkRd: (-1) check_gene_df_type.Rd:18: Lost braces in \itemize; meant \describe ? checkRd: (-1) check_gene_df_type.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) check_gene_df_type.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) check_gene_df_type.Rd:34-35: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:35: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:36-37: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:38: Lost braces 38 | \item{code{list} : \cr}{A \code{list} or character \code{vector}.} | ^ checkRd: (-1) convert_orthologs.Rd:38: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:52: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:53: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:54-55: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:61: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:62: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:63-65: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:66-67: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:68-69: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:101-104: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:105-107: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:108-110: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:111-113: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:114-117: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:118-123: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:156-159: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:160-163: Lost braces in \itemize; meant \describe ? checkRd: (-1) convert_orthologs.Rd:164-167: Lost braces in \itemize; meant \describe ? checkRd: (-1) create_background.Rd:59-62: Lost braces in \itemize; meant \describe ? checkRd: (-1) create_background.Rd:63-65: Lost braces in \itemize; meant \describe ? checkRd: (-1) create_background.Rd:66-68: Lost braces in \itemize; meant \describe ? checkRd: (-1) create_background.Rd:69-71: Lost braces in \itemize; meant \describe ? checkRd: (-1) create_background.Rd:72-75: Lost braces in \itemize; meant \describe ? checkRd: (-1) create_background.Rd:76-81: Lost braces in \itemize; meant \describe ? checkRd: (-1) get_silhouettes.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) get_silhouettes.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) get_silhouettes.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) get_silhouettes.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) gprofiler_namespace.Rd:20: Lost braces 20 | Available namespaces used by link[gprofiler2]{gconvert}. | ^ checkRd: (-1) infer_species.Rd:23: Lost braces in \itemize; meant \describe ? checkRd: (-1) infer_species.Rd:24-25: Lost braces in \itemize; meant \describe ? checkRd: (-1) infer_species.Rd:26: Lost braces 26 | \item{code{list} : \cr}{A \code{list} or character \code{vector}.} | ^ checkRd: (-1) infer_species.Rd:26: Lost braces in \itemize; meant \describe ? checkRd: (-1) infer_species.Rd:40: Lost braces in \itemize; meant \describe ? checkRd: (-1) infer_species.Rd:41: Lost braces in \itemize; meant \describe ? checkRd: (-1) infer_species.Rd:42-43: Lost braces in \itemize; meant \describe ? checkRd: (-1) infer_species.Rd:53: Lost braces in \itemize; meant \describe ? checkRd: (-1) infer_species.Rd:54: Lost braces in \itemize; meant \describe ? checkRd: (-1) infer_species.Rd:55: Lost braces in \itemize; meant \describe ? checkRd: (-1) map_orthologs.Rd:57-60: Lost braces in \itemize; meant \describe ? checkRd: (-1) map_orthologs.Rd:61-64: Lost braces in \itemize; meant \describe ? checkRd: (-1) map_orthologs.Rd:65-68: Lost braces in \itemize; meant \describe ? checkRd: (-1) map_orthologs_custom.Rd:21-24: Lost braces in \itemize; meant \describe ? checkRd: (-1) map_orthologs_custom.Rd:25-28: Lost braces in \itemize; meant \describe ? checkRd: (-1) map_orthologs_custom.Rd:29-32: Lost braces in \itemize; meant \describe ? checkRd: (-1) orthogene-package.Rd:10-11: Lost braces in \itemize; meant \describe ? checkRd: (-1) orthogene-package.Rd:12-13: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_orthotree.Rd:62-64: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_orthotree.Rd:65-67: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_orthotree.Rd:68-71: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_orthotree.Rd:72-74: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_orthotree.Rd:75-76: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_orthotree.Rd:83-86: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_orthotree.Rd:87-89: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_orthotree.Rd:90-92: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_orthotree.Rd:93-95: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_orthotree.Rd:96-99: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_orthotree.Rd:100-105: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_orthotree.Rd:135: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plot_orthotree.Rd:136: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plot_orthotree.Rd:137-138: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plot_orthotree.Rd:139-140: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plot_orthotree.Rd:141: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plot_orthotree.Rd:142: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plot_orthotree.Rd:143: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plot_orthotree.Rd:144: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) prepare_tree.Rd:28-30: Lost braces in \itemize; meant \describe ? checkRd: (-1) prepare_tree.Rd:31-33: Lost braces in \itemize; meant \describe ? checkRd: (-1) prepare_tree.Rd:34-37: Lost braces in \itemize; meant \describe ? checkRd: (-1) prepare_tree.Rd:38-40: Lost braces in \itemize; meant \describe ? checkRd: (-1) prepare_tree.Rd:41-42: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:60-63: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:64-66: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:67-69: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:70-72: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:73-76: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:77-82: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:109: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:110-111: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:112: Lost braces 112 | \item{code{list} : \cr}{A \code{list} or character \code{vector}.} | ^ checkRd: (-1) report_orthologs.Rd:112: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:125: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:126: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:127-128: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:133: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:134: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:135-137: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:138-139: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:140-141: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:180-183: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:184-187: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:188-191: Lost braces in \itemize; meant \describe ? checkRd: (-1) report_orthologs.Rd:204: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) report_orthologs.Rd:205: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) set_gprofiler.Rd:18: 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 'run_benchmark.Rd': 'benchmark_homologene' 'benchmark_gprofiler' 'benchmark_babelgene' 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot_orthotree 53.69 3.53 59.36 prepare_tree 17.21 0.42 17.63 all_genes 4.19 0.17 10.02 convert_orthologs 1.00 0.07 10.52 * 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/orthogene.Rcheck/00check.log' for details.
orthogene.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL orthogene ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'orthogene' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (orthogene)
orthogene.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(orthogene) > > test_check("orthogene") 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 Mapping many:many rows. 1110012L19Rik : converting 1 row(s) --> 2 row(s). 2610034B18Rik : converting 1 row(s) --> 2 row(s). AA415398 : converting 1 row(s) --> 2 row(s). Ankhd1 : converting 1 row(s) --> 2 row(s). Anxa8 : converting 1 row(s) --> 2 row(s). Apitd1 : converting 1 row(s) --> 2 row(s). Arhgap8 : converting 1 row(s) --> 2 row(s). Asb3 : converting 1 row(s) --> 2 row(s). C4a : converting 1 row(s) --> 2 row(s). C4b : converting 1 row(s) --> 2 row(s). Cbs : converting 1 row(s) --> 2 row(s). Ccz1 : converting 1 row(s) --> 2 row(s). Ckmt1 : converting 1 row(s) --> 2 row(s). Coro7 : converting 1 row(s) --> 2 row(s). Cryaa : converting 1 row(s) --> 2 row(s). D10Jhu81e : converting 1 row(s) --> 2 row(s). F8a : converting 1 row(s) --> 3 row(s). Fam21 : converting 1 row(s) --> 2 row(s). Fcgr4 : converting 1 row(s) --> 2 row(s). Gpr89 : converting 1 row(s) --> 2 row(s). Gstt2 : converting 1 row(s) --> 2 row(s). H3f3a : converting 1 row(s) --> 2 row(s). H3f3b : converting 1 row(s) --> 2 row(s). Hspa1a : converting 1 row(s) --> 2 row(s). Icosl : converting 1 row(s) --> 2 row(s). Klhl23 : converting 1 row(s) --> 2 row(s). Mrpl23 : converting 1 row(s) --> 2 row(s). Nbl1 : converting 1 row(s) --> 2 row(s). Nomo1 : converting 1 row(s) --> 3 row(s). Pmf1 : converting 1 row(s) --> 2 row(s). Pom121 : converting 1 row(s) --> 2 row(s). Pramef8 : converting 1 row(s) --> 2 row(s). Prodh : converting 1 row(s) --> 2 row(s). Ranbp2 : converting 1 row(s) --> 7 row(s). Serf1 : converting 1 row(s) --> 2 row(s). Sgk3 : converting 1 row(s) --> 2 row(s). Slx1b : converting 1 row(s) --> 2 row(s). Smn1 : converting 1 row(s) --> 2 row(s). Spin2d : converting 1 row(s) --> 2 row(s). Aggregating rows using: monocle3 Converting obj to sparseMatrix. Matrix aggregated: - Input: 15,259 x 7 - Output: 13,316 x 7 Retrieving all organisms available in gprofiler. Using stored `gprofiler_orgs`. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: mmusculus 477 / 482 (98.96%) genes mapped. Aggregating rows using: monocle3 Converting obj to sparseMatrix. Matrix aggregated: - Input: 482 x 7 - Output: 92 x 7 Converting to DelayedArray. Loading required namespace: DelayedArray Mapping many:many rows. Converting obj to sparseMatrix. 1110012L19Rik : converting 1 row(s) --> 2 row(s). 2610034B18Rik : converting 1 row(s) --> 2 row(s). AA415398 : converting 1 row(s) --> 2 row(s). Ankhd1 : converting 1 row(s) --> 2 row(s). Anxa8 : converting 1 row(s) --> 2 row(s). Apitd1 : converting 1 row(s) --> 2 row(s). Arhgap8 : converting 1 row(s) --> 2 row(s). Asb3 : converting 1 row(s) --> 2 row(s). C4a : converting 1 row(s) --> 2 row(s). C4b : converting 1 row(s) --> 2 row(s). Cbs : converting 1 row(s) --> 2 row(s). Ccz1 : converting 1 row(s) --> 2 row(s). Ckmt1 : converting 1 row(s) --> 2 row(s). Coro7 : converting 1 row(s) --> 2 row(s). Cryaa : converting 1 row(s) --> 2 row(s). D10Jhu81e : converting 1 row(s) --> 2 row(s). F8a : converting 1 row(s) --> 3 row(s). Fam21 : converting 1 row(s) --> 2 row(s). Fcgr4 : converting 1 row(s) --> 2 row(s). Gpr89 : converting 1 row(s) --> 2 row(s). Gstt2 : converting 1 row(s) --> 2 row(s). H3f3a : converting 1 row(s) --> 2 row(s). H3f3b : converting 1 row(s) --> 2 row(s). Hspa1a : converting 1 row(s) --> 2 row(s). Icosl : converting 1 row(s) --> 2 row(s). Klhl23 : converting 1 row(s) --> 2 row(s). Mrpl23 : converting 1 row(s) --> 2 row(s). Nbl1 : converting 1 row(s) --> 2 row(s). Nomo1 : converting 1 row(s) --> 3 row(s). Pmf1 : converting 1 row(s) --> 2 row(s). Pom121 : converting 1 row(s) --> 2 row(s). Pramef8 : converting 1 row(s) --> 2 row(s). Prodh : converting 1 row(s) --> 2 row(s). Ranbp2 : converting 1 row(s) --> 7 row(s). Serf1 : converting 1 row(s) --> 2 row(s). Sgk3 : converting 1 row(s) --> 2 row(s). Slx1b : converting 1 row(s) --> 2 row(s). Smn1 : converting 1 row(s) --> 2 row(s). Spin2d : converting 1 row(s) --> 2 row(s). Aggregating rows using: monocle3 Converting obj to sparseMatrix. Matrix aggregated: - Input: 15,259 x 7 - Output: 13,316 x 7 Converting to DelayedArray. Converting mouse ==> human orthologs using: gprofiler Retrieving all organisms available in gprofiler. Using stored `gprofiler_orgs`. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: mmusculus 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 Mapping many:many rows. Converting obj to sparseMatrix. 1600029O15Rik : converting 1 row(s) --> 2 row(s). 1700030C10Rik : converting 1 row(s) --> 2 row(s). 1700086L19Rik : converting 1 row(s) --> 2 row(s). 1810014B01Rik : converting 1 row(s) --> 2 row(s). 2610005L07Rik : converting 1 row(s) --> 2 row(s). 2810025M15Rik : converting 1 row(s) --> 2 row(s). 2810047C21Rik1 : converting 1 row(s) --> 2 row(s). 4930503E24Rik : converting 1 row(s) --> 2 row(s). 4930519F16Rik : converting 1 row(s) --> 2 row(s). 4931440P22Rik : converting 1 row(s) --> 2 row(s). 4933427D14Rik : converting 1 row(s) --> 2 row(s). 6330549D23Rik : converting 1 row(s) --> 2 row(s). 6820431F20Rik : converting 1 row(s) --> 2 row(s). 9030619P08Rik : converting 1 row(s) --> 2 row(s). A530058N18Rik : converting 1 row(s) --> 2 row(s). Adat3 : converting 1 row(s) --> 2 row(s). Ahcy : converting 1 row(s) --> 2 row(s). Aldoa : converting 1 row(s) --> 2 row(s). Alms1-ps2 : converting 1 row(s) --> 2 row(s). Ap4b1 : converting 1 row(s) --> 2 row(s). Arfip1 : converting 1 row(s) --> 2 row(s). Arhgap26 : converting 1 row(s) --> 2 row(s). Arxes1 : converting 1 row(s) --> 2 row(s). Arxes2 : converting 1 row(s) --> 2 row(s). Asnsd1 : converting 1 row(s) --> 2 row(s). Atn1 : converting 1 row(s) --> 2 row(s). Atp5o : converting 1 row(s) --> 2 row(s). Bfar : converting 1 row(s) --> 2 row(s). Btf3l4 : converting 1 row(s) --> 2 row(s). Calm1 : converting 1 row(s) --> 3 row(s). Calm2 : converting 1 row(s) --> 3 row(s). Calm3 : converting 1 row(s) --> 3 row(s). Cdk2ap1 : converting 1 row(s) --> 2 row(s). Cplx2 : converting 1 row(s) --> 2 row(s). Ctnnd1 : converting 1 row(s) --> 2 row(s). Cycs : converting 1 row(s) --> 2 row(s). Ddit3 : converting 1 row(s) --> 2 row(s). Dohh : converting 1 row(s) --> 2 row(s). Dpep2 : converting 1 row(s) --> 2 row(s). Dpm1 : converting 1 row(s) --> 2 row(s). Eno1 : converting 1 row(s) --> 2 row(s). Erh : converting 1 row(s) --> 2 row(s). Fam220a : converting 1 row(s) --> 2 row(s). Fam78a : converting 1 row(s) --> 2 row(s). Ftl1 : converting 1 row(s) --> 2 row(s). Gcat : converting 1 row(s) --> 2 row(s). Gm10548 : converting 1 row(s) --> 2 row(s). Gm10653 : converting 1 row(s) --> 2 row(s). Gm12238 : converting 1 row(s) --> 2 row(s). Gm14326 : converting 1 row(s) --> 2 row(s). Gm14327 : converting 1 row(s) --> 2 row(s). Gm15760 : converting 1 row(s) --> 2 row(s). Gm16523 : converting 1 row(s) --> 2 row(s). Gm2011 : converting 1 row(s) --> 2 row(s). Gm20257 : converting 1 row(s) --> 2 row(s). Gm3086 : converting 1 row(s) --> 2 row(s). Gm4832 : converting 1 row(s) --> 2 row(s). Gm4956 : converting 1 row(s) --> 2 row(s). Gm5089 : converting 1 row(s) --> 2 row(s). Gm5113 : converting 1 row(s) --> 2 row(s). Gm5124 : converting 1 row(s) --> 2 row(s). Gm5468 : converting 1 row(s) --> 2 row(s). Gm5766 : converting 1 row(s) --> 2 row(s). Gm5885 : converting 1 row(s) --> 2 row(s). Gm6498 : converting 1 row(s) --> 2 row(s). Gm6578 : converting 1 row(s) --> 2 row(s). Gm6793 : converting 1 row(s) --> 2 row(s). Gm7903 : converting 1 row(s) --> 2 row(s). H2-K2 : converting 1 row(s) --> 2 row(s). Hist1h2ad : converting 1 row(s) --> 9 row(s). Hist1h2an : converting 1 row(s) --> 9 row(s). Hmgn2 : converting 1 row(s) --> 2 row(s). Hspa1b : converting 1 row(s) --> 2 row(s). Kpna2 : converting 1 row(s) --> 2 row(s). Lrrc8a : converting 1 row(s) --> 2 row(s). Map2k7 : converting 1 row(s) --> 2 row(s). Mfap1a : converting 1 row(s) --> 2 row(s). Mfap1b : converting 1 row(s) --> 2 row(s). Myef2 : converting 1 row(s) --> 2 row(s). Myl12a : converting 1 row(s) --> 2 row(s). Myl12b : converting 1 row(s) --> 2 row(s). Ndor1 : converting 1 row(s) --> 3 row(s). Nnt : converting 1 row(s) --> 2 row(s). Nrg1 : converting 1 row(s) --> 2 row(s). Nudt10 : converting 1 row(s) --> 2 row(s). Nudt11 : converting 1 row(s) --> 2 row(s). Nudt8 : converting 1 row(s) --> 2 row(s). Nutf2 : converting 1 row(s) --> 2 row(s). Pagr1a : converting 1 row(s) --> 2 row(s). Pam16 : converting 1 row(s) --> 2 row(s). Pde2a : converting 1 row(s) --> 2 row(s). Pfkfb2 : converting 1 row(s) --> 2 row(s). Plp2 : converting 1 row(s) --> 2 row(s). Pms2 : converting 1 row(s) --> 2 row(s). Ppih : converting 1 row(s) --> 2 row(s). Ppp4r1l-ps : converting 1 row(s) --> 2 row(s). Psme2 : converting 1 row(s) --> 2 row(s). Psme2b : converting 1 row(s) --> 2 row(s). Ptp4a1 : converting 1 row(s) --> 2 row(s). Raver1 : converting 1 row(s) --> 2 row(s). Rnasek : converting 1 row(s) --> 2 row(s). Rnaset2a : converting 1 row(s) --> 4 row(s). Rnf26 : converting 1 row(s) --> 2 row(s). Rpl10 : converting 1 row(s) --> 2 row(s). Rpl34-ps1 : converting 1 row(s) --> 2 row(s). Rpl35 : converting 1 row(s) --> 2 row(s). Rpl36a : converting 1 row(s) --> 2 row(s). Rps27 : converting 1 row(s) --> 2 row(s). Rsc1a1 : converting 1 row(s) --> 2 row(s). Serpina3h : converting 1 row(s) --> 2 row(s). Sft2d1 : converting 1 row(s) --> 2 row(s). Slc25a37 : converting 1 row(s) --> 2 row(s). Slc2a4rg-ps : converting 1 row(s) --> 2 row(s). Smok3b : converting 1 row(s) --> 2 row(s). Snhg4 : converting 1 row(s) --> 2 row(s). Snora75 : converting 1 row(s) --> 4 row(s). Snord22 : converting 1 row(s) --> 2 row(s). Snurf : converting 1 row(s) --> 2 row(s). Spag6 : converting 1 row(s) --> 2 row(s). St6galnac2 : converting 1 row(s) --> 2 row(s). Styx : converting 1 row(s) --> 2 row(s). Synj2bp : converting 1 row(s) --> 2 row(s). T2 : converting 1 row(s) --> 2 row(s). Taf9 : converting 1 row(s) --> 2 row(s). Tgtp1 : converting 1 row(s) --> 2 row(s). Timm10b : converting 1 row(s) --> 2 row(s). Tmsb10 : converting 1 row(s) --> 2 row(s). Tuba3a : converting 1 row(s) --> 2 row(s). Txnl4a : converting 1 row(s) --> 2 row(s). U05342 : converting 1 row(s) --> 2 row(s). U2af1l4 : converting 1 row(s) --> 2 row(s). Uba52 : converting 1 row(s) --> 2 row(s). Vmn2r89 : converting 1 row(s) --> 2 row(s). Yy2 : converting 1 row(s) --> 2 row(s). Zbtb9 : converting 1 row(s) --> 2 row(s). Zfp133-ps : converting 1 row(s) --> 2 row(s). Zfp783 : converting 1 row(s) --> 2 row(s). Zfp935 : converting 1 row(s) --> 2 row(s). Zfp939 : converting 1 row(s) --> 2 row(s). Zim3 : converting 1 row(s) --> 2 row(s). Aggregating rows using: stats Converting obj to sparseMatrix. Matrix aggregated: - Input: 15,259 x 7 - Output: 12,617 x 7 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. 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. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: zebrafish Common name mapping found for zebrafish 1 organism identified from search: 7955 Gene table with 20,897 rows retrieved. Returning all 20,897 genes from zebrafish. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: fly Common name mapping found for fly 1 organism identified from search: 7227 Gene table with 8,438 rows retrieved. Returning all 8,438 genes from fly. Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: dmelanogaster 1 organism identified from search: 7227 Preparing babelgene::orthologs_df. Gene table with 20,237 rows retrieved. 20237 Retrieving all genes using: gprofiler Retrieving all organisms available in gprofiler. Using stored `gprofiler_orgs`. Mapping species name: dmelanogaster 1 organism identified from search: dmelanogaster Gene table with 4,606 rows retrieved. 4606 WARNING: In order to set gene_output='rownames' while drop_nonorths=FALSE, must convert gene_df into a sparse matrix. Setting as_sparse=TRUE. WARNING: In order to set gene_output='rownames' while non121_strategy='kbs', must convert gene_df into a sparse matrix. Setting as_sparse=TRUE. Converting to DelayedArray. Preparing gene_df. sparseMatrix format detected. Extracting genes from rownames. 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 Setting ortholog_gene to rownames. Converting obj to sparseMatrix. =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 2,016 / 15,259 (13%) Total genes remaining after convert_orthologs : 13,243 / 15,259 (87%) Preparing gene_df. Dense matrix format detected. Extracting genes from rownames. 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 Setting ortholog_gene to rownames. =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 2,016 / 15,259 (13%) Total genes remaining after convert_orthologs : 13,243 / 15,259 (87%) Preparing gene_df. Dense matrix format detected. Extracting genes from rownames. 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 WARNING: Will convert gene_df from dense matrix to data.frame when gene_output='columns'. Adding input_gene col to gene_df. Adding ortholog_gene col to gene_df. =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 2,016 / 15,259 (13%) Total genes remaining after convert_orthologs : 13,243 / 15,259 (87%) Preparing gene_df. data.frame format detected. Extracting genes from rownames. 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 Adding input_gene col to gene_df. Adding ortholog_gene col to gene_df. =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 2,016 / 15,259 (13%) Total genes remaining after convert_orthologs : 13,243 / 15,259 (87%) Preparing gene_df. data.frame format detected. Preparing gene_df. data.frame format detected. Extracting genes from rownames. 15,259 genes extracted. Converting mouse ==> human orthologs using: homologene Standardising gene names first. Retrieving all organisms available in gprofiler. Using stored `gprofiler_orgs`. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: mmusculus Extracting genes from name. 14,096 genes extracted. 14,096 / 15,259 (92.38%) genes mapped. 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 1:1 orthologs. Filtering gene_df with gene_map Sorting rownames alphanumerically. Adding input_gene col to gene_df. Adding input_gene_standard col to gene_df. Adding ortholog_gene col to gene_df. =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 2,806 / 15,259 (18%) Total genes remaining after convert_orthologs : 12,453 / 15,259 (82%) Preparing gene_df. data.frame format detected. + orthologs previously converted. Detected that gene_df was previously converted to orthologs. Skipping map_orthologs step. Checking for genes without orthologs in human. Extracting genes from input_gene. 12,453 genes extracted. Extracting genes from ortholog_gene. 12,453 genes extracted. Checking for genes without 1:1 orthologs. Dropping 30 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 : 52 / 12,453 (0.42%) Total genes remaining after convert_orthologs : 12,401 / 12,453 (100%) Preparing gene_df. data.frame format detected. Extracting genes from rownames. 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%) Preparing gene_df. character format detected. Converting to data.frame Extracting genes from input_gene. 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 Returning gene_map as dictionary =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 9 / 100 (9%) Total genes remaining after convert_orthologs : 91 / 100 (91%) Preparing gene_df. character format detected. Converting to data.frame Extracting genes from input_gene. 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. =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 9 / 100 (9%) Total genes remaining after convert_orthologs : 91 / 100 (91%) Preparing gene_df. character format detected. Converting to data.frame Extracting genes from input_gene. 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 Adding input_gene col to gene_df. Adding ortholog_gene col to gene_df. =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 9 / 100 (9%) Total genes remaining after convert_orthologs : 91 / 100 (91%) Preparing gene_df. sparseMatrix format detected. Extracting genes from rownames. 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. Filtering gene_df with gene_map Mapping many:many rows. 1110012L19Rik : converting 1 row(s) --> 2 row(s). 2610034B18Rik : converting 1 row(s) --> 2 row(s). AA415398 : converting 1 row(s) --> 2 row(s). Ankhd1 : converting 1 row(s) --> 2 row(s). Anxa8 : converting 1 row(s) --> 2 row(s). Apitd1 : converting 1 row(s) --> 2 row(s). Arhgap8 : converting 1 row(s) --> 2 row(s). Asb3 : converting 1 row(s) --> 2 row(s). C4a : converting 1 row(s) --> 2 row(s). C4b : converting 1 row(s) --> 2 row(s). Cbs : converting 1 row(s) --> 2 row(s). Ccz1 : converting 1 row(s) --> 2 row(s). Ckmt1 : converting 1 row(s) --> 2 row(s). Coro7 : converting 1 row(s) --> 2 row(s). Cryaa : converting 1 row(s) --> 2 row(s). D10Jhu81e : converting 1 row(s) --> 2 row(s). F8a : converting 1 row(s) --> 3 row(s). Fam21 : converting 1 row(s) --> 2 row(s). Fcgr4 : converting 1 row(s) --> 2 row(s). Gpr89 : converting 1 row(s) --> 2 row(s). Gstt2 : converting 1 row(s) --> 2 row(s). H3f3a : converting 1 row(s) --> 2 row(s). H3f3b : converting 1 row(s) --> 2 row(s). Hspa1a : converting 1 row(s) --> 2 row(s). Icosl : converting 1 row(s) --> 2 row(s). Klhl23 : converting 1 row(s) --> 2 row(s). Mrpl23 : converting 1 row(s) --> 2 row(s). Nbl1 : converting 1 row(s) --> 2 row(s). Nomo1 : converting 1 row(s) --> 3 row(s). Pmf1 : converting 1 row(s) --> 2 row(s). Pom121 : converting 1 row(s) --> 2 row(s). Pramef8 : converting 1 row(s) --> 2 row(s). Prodh : converting 1 row(s) --> 2 row(s). Ranbp2 : converting 1 row(s) --> 7 row(s). Serf1 : converting 1 row(s) --> 2 row(s). Sgk3 : converting 1 row(s) --> 2 row(s). Slx1b : converting 1 row(s) --> 2 row(s). Smn1 : converting 1 row(s) --> 2 row(s). Spin2d : converting 1 row(s) --> 2 row(s). Aggregating rows using: monocle3 Converting obj to sparseMatrix. Matrix aggregated: - Input: 13,370 x 7 - Output: 13,316 x 7 =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 1,943 / 15,259 (13%) Total genes remaining after convert_orthologs : 13,316 / 15,259 (87%) Preparing gene_df. sparseMatrix format detected. Extracting genes from rownames. 15,259 genes extracted. Converting mouse ==> human orthologs using: babelgene Retrieving all organisms available in babelgene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: Mus musculus Retrieving all organisms available in babelgene. Mapping species name: human Common name mapping found for human 1 organism identified from search: Homo sapiens Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: Mus musculus 1 organism identified from search: 10090 Preparing babelgene::orthologs_df. Gene table with 29,651 rows retrieved. Checking for genes without orthologs in human. Extracting genes from input_gene. 29,651 genes extracted. Dropping 37 NAs of all kinds from input_gene. Extracting genes from ortholog_gene. 29,614 genes extracted. Dropping 146 NAs of all kinds from ortholog_gene. Checking for genes without 1:1 orthologs. Dropping 9,286 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 10,297 genes that have multiple ortholog_gene per input_gene (1:many). Filtering gene_df with gene_map Setting ortholog_gene to rownames. =========== REPORT SUMMARY =========== Total genes dropped after convert_orthologs : 4,000 / 15,259 (26%) Total genes remaining after convert_orthologs : 11,259 / 15,259 (74%) Preparing gene_df. sparseMatrix format detected. Extracting genes from rownames. 15,259 genes extracted. Converting mouse ==> mouse 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: mouse Common name mapping found for mouse 1 organism identified from search: 10090 input_species already formatted as output species. Returning input data directly. Preparing gene_df. DelayedArray format detected. Extracting genes from rownames. 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 Setting ortholog_gene to rownames. =========== 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 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. Generating gene background for mouse x rat ==> rat Gathering ortholog reports. 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. -- 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 ==> rat 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: 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. 20,872 genes extracted. Extracting genes from ortholog_gene. 20,872 genes extracted. Checking for genes without 1:1 orthologs. Dropping 2,075 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 1,975 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 : 4,186 / 21,207 (20%) Total genes remaining after convert_orthologs : 17,021 / 21,207 (80%) -- =========== REPORT SUMMARY =========== 17,021 / 21,207 (80.26%) target_species genes remain after ortholog conversion. 17,021 / 20,616 (82.56%) reference_species genes remain after ortholog conversion. Gathering ortholog reports. 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. -- 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. -- =========== REPORT SUMMARY =========== 20,616 / 20,616 (100%) target_species genes remain after ortholog conversion. 20,616 / 20,616 (100%) reference_species genes remain after ortholog conversion. 17,021 intersect background genes used. 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. Returning 20,616 unique genes from entire rat genome. Generating gene background for human x rat ==> mouse Gathering ortholog reports. 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. -- 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. -- -- Preparing gene_df. data.frame format detected. Extracting genes from Gene.Symbol. 19,129 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. 17,355 genes extracted. Extracting genes from ortholog_gene. 17,355 genes extracted. Checking for genes without 1:1 orthologs. Dropping 498 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 131 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 : 2,647 / 19,129 (14%) Total genes remaining after convert_orthologs : 16,482 / 19,129 (86%) -- =========== REPORT SUMMARY =========== 16,482 / 19,129 (86.16%) target_species genes remain after ortholog conversion. 16,482 / 21,207 (77.72%) reference_species genes remain after ortholog conversion. Gathering ortholog reports. 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. -- 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 ==> mouse 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: 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. 20,872 genes extracted. Extracting genes from ortholog_gene. 20,872 genes extracted. Checking for genes without 1:1 orthologs. Dropping 1,975 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 2,075 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 : 3,595 / 20,616 (17%) Total genes remaining after convert_orthologs : 17,021 / 20,616 (83%) -- =========== REPORT SUMMARY =========== 17,021 / 20,616 (82.56%) target_species genes remain after ortholog conversion. 17,021 / 21,207 (80.26%) reference_species genes remain after ortholog conversion. 15,450 intersect background genes used. Generating gene background for monkey x chimp ==> 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. -- chimp Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: chimp Common name mapping found for chimp 1 organism identified from search: 9598 Gene table with 18,730 rows retrieved. Returning all 18,730 genes from chimp. -- -- Preparing gene_df. data.frame format detected. Extracting genes from Gene.Symbol. 18,730 genes extracted. Converting chimp ==> human orthologs using: homologene Retrieving all organisms available in homologene. Mapping species name: chimp Common name mapping found for chimp 1 organism identified from search: 9598 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. 17,737 genes extracted. Extracting genes from ortholog_gene. 17,737 genes extracted. Checking for genes without 1:1 orthologs. Dropping 257 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 151 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 : 1,506 / 18,703 (8.1%) Total genes remaining after convert_orthologs : 17,197 / 18,703 (92%) -- =========== REPORT SUMMARY =========== 17,185 / 18,703 (91.88%) target_species genes remain after ortholog conversion. 17,185 / 19,129 (89.84%) reference_species genes remain after ortholog conversion. 14,190 intersect background genes used. ===== mouse tests ===== Preparing gene_df. sparseMatrix format detected. Extracting genes from rownames. 200 genes extracted. Testing for gene overlap with: 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. Testing for gene overlap with: 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. Testing for gene overlap with: 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. Testing for gene overlap with: 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. Testing for gene overlap with: zebrafish Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: zebrafish Common name mapping found for zebrafish 1 organism identified from search: 7955 Gene table with 20,897 rows retrieved. Returning all 20,897 genes from zebrafish. Testing for gene overlap with: fly Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: fly Common name mapping found for fly 1 organism identified from search: 7227 Gene table with 8,438 rows retrieved. Returning all 8,438 genes from fly. Top match: - species: mouse - percent_match: 96% ===== mouse tests2 ===== Preparing gene_df. character format detected. Converting to data.frame Extracting genes from input_gene. 200 genes extracted. Testing for gene overlap with: 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. Testing for gene overlap with: 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. Testing for gene overlap with: 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. Testing for gene overlap with: 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. Testing for gene overlap with: zebrafish Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: zebrafish Common name mapping found for zebrafish 1 organism identified from search: 7955 Gene table with 20,897 rows retrieved. Returning all 20,897 genes from zebrafish. Testing for gene overlap with: fly Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: fly Common name mapping found for fly 1 organism identified from search: 7227 Gene table with 8,438 rows retrieved. Returning all 8,438 genes from fly. Top match: - species: mouse - percent_match: 96% ===== human tests ===== Preparing gene_df. character format detected. Converting to data.frame Extracting genes from input_gene. 100 genes extracted. Testing for gene overlap with: 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. Testing for gene overlap with: 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. Testing for gene overlap with: 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. Testing for gene overlap with: 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. Testing for gene overlap with: zebrafish Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: zebrafish Common name mapping found for zebrafish 1 organism identified from search: 7955 Gene table with 20,897 rows retrieved. Returning all 20,897 genes from zebrafish. Testing for gene overlap with: fly Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: fly Common name mapping found for fly 1 organism identified from search: 7227 Gene table with 8,438 rows retrieved. Returning all 8,438 genes from fly. Top match: - species: human - percent_match: 98% ===== mouse tests ===== Preparing gene_df. sparseMatrix format detected. Extracting genes from rownames. 200 genes extracted. Testing for gene overlap with: human Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Preparing babelgene::orthologs_df. Gene table with 20,492 rows retrieved. Returning all 20,492 genes from human. Testing for gene overlap with: monkey Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: monkey Common name mapping found for monkey 1 organism identified from search: 9544 Preparing babelgene::orthologs_df. Gene table with 20,402 rows retrieved. Returning all 20,402 genes from monkey. Testing for gene overlap with: rat Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: rat Common name mapping found for rat 1 organism identified from search: 10116 Preparing babelgene::orthologs_df. Gene table with 21,427 rows retrieved. Returning all 21,427 genes from rat. Testing for gene overlap with: mouse Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Preparing babelgene::orthologs_df. Gene table with 29,651 rows retrieved. Returning all 29,651 genes from mouse. Testing for gene overlap with: zebrafish Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: zebrafish Common name mapping found for zebrafish 1 organism identified from search: 7955 Preparing babelgene::orthologs_df. Gene table with 30,886 rows retrieved. Returning all 30,886 genes from zebrafish. Testing for gene overlap with: fly Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: fly Common name mapping found for fly 1 organism identified from search: 7227 Preparing babelgene::orthologs_df. Gene table with 20,237 rows retrieved. Returning all 20,237 genes from fly. Top match: - species: mouse - percent_match: 89% ===== mouse tests2 ===== Preparing gene_df. character format detected. Converting to data.frame Extracting genes from input_gene. 200 genes extracted. Testing for gene overlap with: human Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Preparing babelgene::orthologs_df. Gene table with 20,492 rows retrieved. Returning all 20,492 genes from human. Testing for gene overlap with: monkey Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: monkey Common name mapping found for monkey 1 organism identified from search: 9544 Preparing babelgene::orthologs_df. Gene table with 20,402 rows retrieved. Returning all 20,402 genes from monkey. Testing for gene overlap with: rat Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: rat Common name mapping found for rat 1 organism identified from search: 10116 Preparing babelgene::orthologs_df. Gene table with 21,427 rows retrieved. Returning all 21,427 genes from rat. Testing for gene overlap with: mouse Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Preparing babelgene::orthologs_df. Gene table with 29,651 rows retrieved. Returning all 29,651 genes from mouse. Testing for gene overlap with: zebrafish Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: zebrafish Common name mapping found for zebrafish 1 organism identified from search: 7955 Preparing babelgene::orthologs_df. Gene table with 30,886 rows retrieved. Returning all 30,886 genes from zebrafish. Testing for gene overlap with: fly Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: fly Common name mapping found for fly 1 organism identified from search: 7227 Preparing babelgene::orthologs_df. Gene table with 20,237 rows retrieved. Returning all 20,237 genes from fly. Top match: - species: mouse - percent_match: 89% ===== human tests ===== Preparing gene_df. character format detected. Converting to data.frame Extracting genes from input_gene. 100 genes extracted. Testing for gene overlap with: human Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Preparing babelgene::orthologs_df. Gene table with 20,492 rows retrieved. Returning all 20,492 genes from human. Testing for gene overlap with: monkey Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: monkey Common name mapping found for monkey 1 organism identified from search: 9544 Preparing babelgene::orthologs_df. Gene table with 20,402 rows retrieved. Returning all 20,402 genes from monkey. Testing for gene overlap with: rat Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: rat Common name mapping found for rat 1 organism identified from search: 10116 Preparing babelgene::orthologs_df. Gene table with 21,427 rows retrieved. Returning all 21,427 genes from rat. Testing for gene overlap with: mouse Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Preparing babelgene::orthologs_df. Gene table with 29,651 rows retrieved. Returning all 29,651 genes from mouse. Testing for gene overlap with: zebrafish Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: zebrafish Common name mapping found for zebrafish 1 organism identified from search: 7955 Preparing babelgene::orthologs_df. Gene table with 30,886 rows retrieved. Returning all 30,886 genes from zebrafish. Testing for gene overlap with: fly Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: fly Common name mapping found for fly 1 organism identified from search: 7227 Preparing babelgene::orthologs_df. Gene table with 20,237 rows retrieved. Returning all 20,237 genes from fly. Top match: - species: human - percent_match: 100% Loading local .RDS file. Loading local .RDA file. 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 Extracting genes from name. 3 genes extracted. 3 / 9 (33.33%) genes mapped. Retrieving all organisms available in gprofiler. Using stored `gprofiler_orgs`. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: mmusculus Extracting genes from name. 7 genes extracted. 7 / 9 (77.78%) genes mapped. Retrieving all organisms available in gprofiler. Using stored `gprofiler_orgs`. Mapping species name: zebrafish Common name mapping found for zebrafish 1 organism identified from search: drerio Extracting genes from name. 3 genes extracted. 3 / 9 (33.33%) genes mapped. Retrieving all organisms available in gprofiler. Using stored `gprofiler_orgs`. Mapping species name: fly Common name mapping found for fly 1 organism identified from search: dmelanogaster Extracting genes from name. 78 genes extracted. 78 / 1,000 (7.8%) genes mapped. Retrieving all organisms available in gprofiler. Using stored `gprofiler_orgs`. Mapping species name: Schmidtea mediterranea 2 organisms identified from search. Selecting first: - scmediprjna12585 - scmediprjna379262 Mapping genes with Planosphere. Extracting genes from name. 3 genes extracted. Dropping 1 NAs of all kinds from name. 2 / 3 (66.67%) genes mapped. Retrieving all organisms available in babelgene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: Mus musculus Retrieving all organisms available in babelgene. Mapping species name: human Common name mapping found for human 1 organism identified from search: Homo sapiens Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: Mus musculus 1 organism identified from search: 10090 Preparing babelgene::orthologs_df. Gene table with 29,651 rows retrieved. Retrieving all organisms available in babelgene. Mapping species name: human Common name mapping found for human 1 organism identified from search: Homo sapiens Retrieving all organisms available in babelgene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: Mus musculus Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: Mus musculus 1 organism identified from search: 10090 Preparing babelgene::orthologs_df. Gene table with 29,651 rows retrieved. Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: zebrafish Common name mapping found for zebrafish 1 organism identified from search: 7955 Preparing babelgene::orthologs_df. Gene table with 30,886 rows retrieved. Returning all 30,886 genes from zebrafish. Retrieving all organisms available in babelgene. Mapping species name: zebrafish Common name mapping found for zebrafish 1 organism identified from search: Danio rerio Retrieving all organisms available in babelgene. Mapping species name: human Common name mapping found for human 1 organism identified from search: Homo sapiens Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: Danio rerio 1 organism identified from search: 7955 Preparing babelgene::orthologs_df. Gene table with 30,886 rows retrieved. Retrieving all organisms available in babelgene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: Mus musculus Retrieving all organisms available in babelgene. Mapping species name: Gallus gallus 1 organism identified from search: Gallus gallus Retrieving all organisms available in babelgene. Mapping species name: human Common name mapping found for human 1 organism identified from search: Homo sapiens Retrieving all organisms available in babelgene. Mapping species name: human Common name mapping found for human 1 organism identified from search: Homo sapiens Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: Homo sapiens Mapping species name: 9544 1 organism identified from search: Macaca mulatta Mapping species name: mus musculus 1 organism identified from search: Mus musculus Mapping species name: fruit fly Common name mapping found for fruit fly 1 organism identified from search: Drosophila melanogaster Mapping species name: Celegans 1 organism identified from search: Caenorhabditis elegans method='grpofiler' not recognized by get_all_orgs. Defaulting to 'gprofiler'. Using stored `gprofiler_orgs`. Mapping species name: human Common name mapping found for human 1 organism identified from search: hsapiens Mapping species name: 9544 1 organism identified from search: mmulatta Mapping species name: mus musculus 1 organism identified from search: mmusculus Mapping species name: fruit fly Common name mapping found for fruit fly 1 organism identified from search: dmelanogaster Mapping species name: Celegans 1 organism identified from search: celegans Retrieving all organisms available in homologene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Mapping species name: 9544 1 organism identified from search: 9544 Mapping species name: mus musculus 1 organism identified from search: 10090 Mapping species name: fruit fly Common name mapping found for fruit fly 1 organism identified from search: 7227 Mapping species name: Celegans 1 organism identified from search: 6239 Retrieving all organisms available in homologene. `geom_smooth()` using formula = 'y ~ x' Gathering ortholog reports. Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: Homo sapiens 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from Homo sapiens. -- human Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: Homo sapiens 1 organism identified from search: 9606 Gene table with 19,129 rows retrieved. Returning all 19,129 genes from Homo sapiens. -- =========== 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. -- 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 ==> Homo sapiens 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: Homo sapiens 1 organism identified from search: 9606 Checking for genes without orthologs in Homo sapiens. 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. -- 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 ==> Homo sapiens 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: Homo sapiens 1 organism identified from search: 9606 Checking for genes without orthologs in Homo sapiens. 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. Loading required namespace: phytools Loading required namespace: TreeTools Importing tree from: TimeTree2022 Importing cached tree. Standardising tip labels. Mapping 3 species from `species`. Mapping 3 species from tree. -- 0/3 (0%) tips dropped from tree due to inability to standardise names with `map_species`. -- 0/3 (0%) tips dropped from tree according to overlap with selected `species`. Loading required namespace: rphylopic Gathering phylopic silhouettes. + homo sapiens + macaca mulatta + mus musculus Preparing data for 6 clades. Warning: Each clade in `clades` must contain a vector of at least 1 species. Omitting clade: Invertebrates 3 species remaining after metadata preparation. Loading required namespace: ggimage Creating ggtree plot. Saving plot ==> F:\biocbuild\bbs-3.20-bioc\tmpdir\Rtmp6VRPqZ\file1f0e08e95a08.ggtree.pdf Saving plot ==> F:\biocbuild\bbs-3.20-bioc\tmpdir\Rtmp6VRPqZ\file1f0e037c6ed.ggtree.png Gathering ortholog reports. Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: Homo sapiens 1 organism identified from search: 9606 Preparing babelgene::orthologs_df. Gene table with 20,492 rows retrieved. Returning all 20,492 genes from Homo sapiens. -- human Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: Homo sapiens 1 organism identified from search: 9606 Preparing babelgene::orthologs_df. Gene table with 20,492 rows retrieved. Returning all 20,492 genes from Homo sapiens. -- =========== REPORT SUMMARY =========== 20,206 / 20,206 (100%) target_species genes remain after ortholog conversion. 20,206 / 20,206 (100%) reference_species genes remain after ortholog conversion. -- monkey Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: monkey Common name mapping found for monkey 1 organism identified from search: 9544 Preparing babelgene::orthologs_df. Gene table with 20,402 rows retrieved. Returning all 20,402 genes from monkey. -- -- Preparing gene_df. data.frame format detected. Extracting genes from Gene.Symbol. 20,402 genes extracted. Converting monkey ==> Homo sapiens orthologs using: babelgene Retrieving all organisms available in babelgene. Mapping species name: monkey Common name mapping found for monkey 1 organism identified from search: Macaca mulatta Retrieving all organisms available in babelgene. Mapping species name: Homo sapiens 1 organism identified from search: Homo sapiens Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: Macaca mulatta 1 organism identified from search: 9544 Preparing babelgene::orthologs_df. Gene table with 20,402 rows retrieved. Checking for genes without orthologs in Homo sapiens. Extracting genes from input_gene. 20,402 genes extracted. Dropping 561 NAs of all kinds from input_gene. Extracting genes from ortholog_gene. 19,841 genes extracted. Dropping 107 NAs of all kinds from ortholog_gene. Checking for genes without 1:1 orthologs. Dropping 1,371 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 1,000 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 : 1,452 / 18,149 (8%) Total genes remaining after convert_orthologs : 16,697 / 18,149 (92%) -- =========== REPORT SUMMARY =========== 16,459 / 18,149 (90.69%) target_species genes remain after ortholog conversion. 16,459 / 20,206 (81.46%) reference_species genes remain after ortholog conversion. -- mouse Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Preparing babelgene::orthologs_df. Gene table with 29,651 rows retrieved. Returning all 29,651 genes from mouse. -- -- Preparing gene_df. data.frame format detected. Extracting genes from Gene.Symbol. 29,651 genes extracted. Converting mouse ==> Homo sapiens orthologs using: babelgene Retrieving all organisms available in babelgene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: Mus musculus Retrieving all organisms available in babelgene. Mapping species name: Homo sapiens 1 organism identified from search: Homo sapiens Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: Mus musculus 1 organism identified from search: 10090 Preparing babelgene::orthologs_df. Gene table with 29,651 rows retrieved. Checking for genes without orthologs in Homo sapiens. Extracting genes from input_gene. 29,651 genes extracted. Dropping 37 NAs of all kinds from input_gene. Extracting genes from ortholog_gene. 29,614 genes extracted. Dropping 146 NAs of all kinds from ortholog_gene. Checking for genes without 1:1 orthologs. Dropping 9,286 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 10,297 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 : 4,602 / 20,075 (23%) Total genes remaining after convert_orthologs : 15,473 / 20,075 (77%) -- =========== REPORT SUMMARY =========== 15,314 / 20,075 (76.28%) target_species genes remain after ortholog conversion. 15,314 / 20,206 (75.79%) reference_species genes remain after ortholog conversion. Importing tree from: TimeTree2022 Importing cached tree. Standardising tip labels. Mapping 3 species from `species`. Mapping 3 species from tree. -- 0/3 (0%) tips dropped from tree due to inability to standardise names with `map_species`. -- 0/3 (0%) tips dropped from tree according to overlap with selected `species`. Gathering phylopic silhouettes. + homo sapiens + macaca mulatta + mus musculus Preparing data for 6 clades. Warning: Each clade in `clades` must contain a vector of at least 1 species. Omitting clade: Invertebrates 3 species remaining after metadata preparation. Creating ggtree plot. Saving plot ==> F:\biocbuild\bbs-3.20-bioc\tmpdir\Rtmp6VRPqZ\file1f0e014d56374.ggtree.pdf Saving plot ==> F:\biocbuild\bbs-3.20-bioc\tmpdir\Rtmp6VRPqZ\file1f0e075e151aa.ggtree.png Importing tree from: TimeTree2022 Importing cached tree. Standardising tip labels. Mapping 3 species from `species`. Mapping 3 species from tree. -- 0/3 (0%) tips dropped from tree due to inability to standardise names with `map_species`. -- 0/3 (0%) tips dropped from tree according to overlap with selected `species`. 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. -- zebrafish Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: zebrafish Common name mapping found for zebrafish 1 organism identified from search: 7955 Gene table with 20,897 rows retrieved. Returning all 20,897 genes from zebrafish. -- -- Preparing gene_df. data.frame format detected. Extracting genes from Gene.Symbol. 20,897 genes extracted. Converting zebrafish ==> human orthologs using: homologene Retrieving all organisms available in homologene. Mapping species name: zebrafish Common name mapping found for zebrafish 1 organism identified from search: 7955 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. 14,768 genes extracted. Extracting genes from ortholog_gene. 14,768 genes extracted. Checking for genes without 1:1 orthologs. Dropping 46 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 2,707 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 : 10,336 / 20,895 (49%) Total genes remaining after convert_orthologs : 10,559 / 20,895 (51%) -- =========== REPORT SUMMARY =========== 10,557 / 20,895 (50.52%) target_species genes remain after ortholog conversion. 10,557 / 19,129 (55.19%) 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. -- fly Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: fly Common name mapping found for fly 1 organism identified from search: 7227 Gene table with 8,438 rows retrieved. Returning all 8,438 genes from fly. -- -- Preparing gene_df. data.frame format detected. Extracting genes from Gene.Symbol. 8,438 genes extracted. Converting fly ==> human orthologs using: homologene Retrieving all organisms available in homologene. Mapping species name: fly Common name mapping found for fly 1 organism identified from search: 7227 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. 4,500 genes extracted. Dropping 1 NAs of all kinds from input_gene. Extracting genes from ortholog_gene. 4,499 genes extracted. Checking for genes without 1:1 orthologs. Dropping 19 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 266 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 : 4,380 / 8,438 (52%) Total genes remaining after convert_orthologs : 4,058 / 8,438 (48%) -- =========== REPORT SUMMARY =========== 4,058 / 8,438 (48.09%) target_species genes remain after ortholog conversion. 4,058 / 19,129 (21.21%) 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. Gathering ortholog reports. Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Preparing babelgene::orthologs_df. Gene table with 20,492 rows retrieved. Returning all 20,492 genes from human. -- mouse Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: 10090 Preparing babelgene::orthologs_df. Gene table with 29,651 rows retrieved. Returning all 29,651 genes from mouse. -- -- Preparing gene_df. data.frame format detected. Extracting genes from Gene.Symbol. 29,651 genes extracted. Converting mouse ==> human orthologs using: babelgene Retrieving all organisms available in babelgene. Mapping species name: mouse Common name mapping found for mouse 1 organism identified from search: Mus musculus Retrieving all organisms available in babelgene. Mapping species name: human Common name mapping found for human 1 organism identified from search: Homo sapiens Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: Mus musculus 1 organism identified from search: 10090 Preparing babelgene::orthologs_df. Gene table with 29,651 rows retrieved. Checking for genes without orthologs in human. Extracting genes from input_gene. 29,651 genes extracted. Dropping 37 NAs of all kinds from input_gene. Extracting genes from ortholog_gene. 29,614 genes extracted. Dropping 146 NAs of all kinds from ortholog_gene. Checking for genes without 1:1 orthologs. Dropping 9,286 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 10,297 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 : 4,602 / 20,075 (23%) Total genes remaining after convert_orthologs : 15,473 / 20,075 (77%) -- =========== REPORT SUMMARY =========== 15,314 / 20,075 (76.28%) target_species genes remain after ortholog conversion. 15,314 / 20,206 (75.79%) reference_species genes remain after ortholog conversion. Gathering ortholog reports. Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Preparing babelgene::orthologs_df. Gene table with 20,492 rows retrieved. Returning all 20,492 genes from human. -- zebrafish Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: zebrafish Common name mapping found for zebrafish 1 organism identified from search: 7955 Preparing babelgene::orthologs_df. Gene table with 30,886 rows retrieved. Returning all 30,886 genes from zebrafish. -- -- Preparing gene_df. data.frame format detected. Extracting genes from Gene.Symbol. 30,886 genes extracted. Converting zebrafish ==> human orthologs using: babelgene Retrieving all organisms available in babelgene. Mapping species name: zebrafish Common name mapping found for zebrafish 1 organism identified from search: Danio rerio Retrieving all organisms available in babelgene. Mapping species name: human Common name mapping found for human 1 organism identified from search: Homo sapiens Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: Danio rerio 1 organism identified from search: 7955 Preparing babelgene::orthologs_df. Gene table with 30,886 rows retrieved. Checking for genes without orthologs in human. Extracting genes from input_gene. 30,886 genes extracted. Dropping 10 NAs of all kinds from input_gene. Extracting genes from ortholog_gene. 30,876 genes extracted. Dropping 70 NAs of all kinds from ortholog_gene. Checking for genes without 1:1 orthologs. Dropping 10,855 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 14,453 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 : 11,805 / 19,781 (60%) Total genes remaining after convert_orthologs : 7,976 / 19,781 (40%) -- =========== REPORT SUMMARY =========== 7,860 / 19,781 (39.74%) target_species genes remain after ortholog conversion. 7,860 / 20,206 (38.9%) reference_species genes remain after ortholog conversion. Gathering ortholog reports. Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Preparing babelgene::orthologs_df. Gene table with 20,492 rows retrieved. Returning all 20,492 genes from human. -- fly Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: fly Common name mapping found for fly 1 organism identified from search: 7227 Preparing babelgene::orthologs_df. Gene table with 20,237 rows retrieved. Returning all 20,237 genes from fly. -- -- Preparing gene_df. data.frame format detected. Extracting genes from Gene.Symbol. 20,237 genes extracted. Converting fly ==> human orthologs using: babelgene Retrieving all organisms available in babelgene. Mapping species name: fly Common name mapping found for fly 1 organism identified from search: Drosophila melanogaster Retrieving all organisms available in babelgene. Mapping species name: human Common name mapping found for human 1 organism identified from search: Homo sapiens Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: Drosophila melanogaster 1 organism identified from search: 7227 Preparing babelgene::orthologs_df. Gene table with 20,237 rows retrieved. Checking for genes without orthologs in human. Extracting genes from input_gene. 20,237 genes extracted. Dropping 7 NAs of all kinds from input_gene. Extracting genes from ortholog_gene. 20,230 genes extracted. Dropping 32 NAs of all kinds from ortholog_gene. Checking for genes without 1:1 orthologs. Dropping 11,721 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 9,141 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 : 5,175 / 8,471 (61%) Total genes remaining after convert_orthologs : 3,296 / 8,471 (39%) -- =========== REPORT SUMMARY =========== 3,276 / 8,471 (38.67%) target_species genes remain after ortholog conversion. 3,276 / 20,206 (16.21%) reference_species genes remain after ortholog conversion. Gathering ortholog reports. Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Preparing babelgene::orthologs_df. Gene table with 20,492 rows retrieved. Returning all 20,492 genes from human. -- human Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: human Common name mapping found for human 1 organism identified from search: 9606 Preparing babelgene::orthologs_df. Gene table with 20,492 rows retrieved. Returning all 20,492 genes from human. -- =========== REPORT SUMMARY =========== 20,206 / 20,206 (100%) target_species genes remain after ortholog conversion. 20,206 / 20,206 (100%) 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. -- 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. ==== fruit fly ==== ------- Benchmarking homologene ------- Benchmarking all_genes() Retrieving all genes using: homologene. Retrieving all organisms available in homologene. Mapping species name: fruit fly Common name mapping found for fruit fly 1 organism identified from search: 7227 Gene table with 8,438 rows retrieved. Extracting genes from Gene.Symbol. 8,438 genes extracted. Dropping 2 NAs of all kinds from Gene.Symbol. Returning all 8,436 genes from fruit fly. Benchmarking convert_orthologs() Preparing gene_df. data.frame format detected. Extracting genes from Gene.Symbol. 8,436 genes extracted. Converting fruit fly ==> human orthologs using: homologene Retrieving all organisms available in homologene. Mapping species name: fruit fly Common name mapping found for fruit fly 1 organism identified from search: 7227 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. 4,499 genes extracted. Extracting genes from ortholog_gene. 4,499 genes extracted. Checking for genes without 1:1 orthologs. Dropping 19 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 266 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 : 4,378 / 8,436 (52%) Total genes remaining after convert_orthologs : 4,058 / 8,436 (48%) ------- Benchmarking gprofiler ------- Benchmarking all_genes() Retrieving all genes using: gprofiler Retrieving all organisms available in gprofiler. Using stored `gprofiler_orgs`. Mapping species name: fruit fly Common name mapping found for fruit fly 1 organism identified from search: dmelanogaster Gene table with 4,606 rows retrieved. Extracting genes from Gene.Symbol. 4,606 genes extracted. Dropping 1 NAs of all kinds from Gene.Symbol. Returning all 4,605 genes from fruit fly. Benchmarking convert_orthologs() Preparing gene_df. data.frame format detected. Extracting genes from Gene.Symbol. 4,605 genes extracted. Converting fruit fly ==> human orthologs using: gprofiler Retrieving all organisms available in gprofiler. Using stored `gprofiler_orgs`. Mapping species name: fruit fly Common name mapping found for fruit fly 1 organism identified from search: dmelanogaster 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 Checking for genes without orthologs in human. Extracting genes from input_gene. 6,480 genes extracted. Extracting genes from ortholog_gene. 6,480 genes extracted. Dropping 3,440 NAs of all kinds from ortholog_gene. Checking for genes without 1:1 orthologs. Dropping 1,871 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 768 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 : 3,958 / 4,605 (86%) Total genes remaining after convert_orthologs : 647 / 4,605 (14%) ------- Benchmarking babelgene ------- Benchmarking all_genes() Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: fruit fly Common name mapping found for fruit fly 1 organism identified from search: 7227 Preparing babelgene::orthologs_df. Gene table with 20,237 rows retrieved. Extracting genes from Gene.Symbol. 20,237 genes extracted. Dropping 7 NAs of all kinds from Gene.Symbol. Returning all 20,230 genes from fruit fly. Benchmarking convert_orthologs() Preparing gene_df. data.frame format detected. Extracting genes from Gene.Symbol. 20,230 genes extracted. Converting fruit fly ==> human orthologs using: babelgene Retrieving all organisms available in babelgene. Mapping species name: fruit fly Common name mapping found for fruit fly 1 organism identified from search: Drosophila melanogaster Retrieving all organisms available in babelgene. Mapping species name: human Common name mapping found for human 1 organism identified from search: Homo sapiens Retrieving all genes using: babelgene. Retrieving all organisms available in babelgene. Mapping species name: Drosophila melanogaster 1 organism identified from search: 7227 Preparing babelgene::orthologs_df. Gene table with 20,237 rows retrieved. Checking for genes without orthologs in human. Extracting genes from input_gene. 20,237 genes extracted. Dropping 7 NAs of all kinds from input_gene. Extracting genes from ortholog_gene. 20,230 genes extracted. Dropping 32 NAs of all kinds from ortholog_gene. Checking for genes without 1:1 orthologs. Dropping 11,721 genes that have multiple input_gene per ortholog_gene (many:1). Dropping 9,141 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 : 5,173 / 8,469 (61%) Total genes remaining after convert_orthologs : 3,296 / 8,469 (39%) Finished fruit fly in 0.245 minutes. Saving benchmarking results ==> F:\biocbuild\bbs-3.20-bioc\tmpdir\Rtmp6VRPqZ\file1f0e071983eef.csv WARNING: Species 'monkeytypo' not found in taxa dict. [ FAIL 0 | WARN 3 | SKIP 0 | PASS 155 ] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 155 ] > > proc.time() user system elapsed 328.62 14.78 380.57
orthogene.Rcheck/orthogene-Ex.timings
name | user | system | elapsed | |
aggregate_mapped_genes | 1.92 | 0.16 | 3.28 | |
all_genes | 4.19 | 0.17 | 10.02 | |
all_species | 0.07 | 0.01 | 0.08 | |
convert_orthologs | 1.00 | 0.07 | 10.52 | |
create_background | 1.50 | 0.01 | 1.78 | |
format_species | 0.01 | 0.00 | 0.01 | |
get_silhouettes | 0.95 | 0.89 | 2.38 | |
infer_species | 0.58 | 0.05 | 0.62 | |
map_genes | 0.07 | 0.00 | 0.35 | |
map_orthologs | 0.89 | 0.05 | 4.12 | |
map_species | 0.06 | 0.00 | 0.06 | |
plot_orthotree | 53.69 | 3.53 | 59.36 | |
prepare_tree | 17.21 | 0.42 | 17.63 | |
report_orthologs | 0.63 | 0.02 | 0.69 | |