##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:orthogene.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings orthogene_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/orthogene.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'orthogene/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'orthogene' version '1.2.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package '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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'DelayedMatrixStats'
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'aggregate_rows'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking 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         19.65   0.44   35.70
prepare_tree           11.89   0.12   12.17
all_genes               4.66   0.17   17.11
aggregate_mapped_genes  2.28   0.13    5.46
convert_orthologs       0.99   0.03    6.34
map_orthologs           0.85   0.00    6.26
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'F:/biocbuild/bbs-3.15-bioc/meat/orthogene.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL orthogene
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-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)

R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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: 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
nrow(gene_map) > nrow(gene_df)
Checking for genes without 1:1 orthologs.
Dropping 2,998 genes that have multiple ortholog_gene per input_gene.
Extracting genes from input_gene.
12,801 genes extracted.
Extracting genes from ortholog_gene.
12,801 genes extracted.
Aggregating rows using: monocle3
Matrix aggregated:
  - Input: 12,801 x 7 
  - Output: 12,801 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
482 / 482 (100%) genes mapped.
Aggregating rows using: monocle3
Matrix aggregated:
  - Input: 482 x 7 
  - Output: 92 x 7
Loading required namespace: DelayedArray
Converting to DelayedArray.
nrow(gene_map) > nrow(gene_df)
Checking for genes without 1:1 orthologs.
Dropping 2,998 genes that have multiple ortholog_gene per input_gene.
Extracting genes from input_gene.
12,801 genes extracted.
Extracting genes from ortholog_gene.
12,801 genes extracted.
Aggregating rows using: monocle3
Matrix aggregated:
  - Input: 12,801 x 7 
  - Output: 12,801 x 7
Converting to DelayedArray.
nrow(gene_map) > nrow(gene_df)
Checking for genes without 1:1 orthologs.
Dropping 2,998 genes that have multiple ortholog_gene per input_gene.
Extracting genes from input_gene.
12,801 genes extracted.
Extracting genes from ortholog_gene.
12,801 genes extracted.
Aggregating rows using: stats
Matrix aggregated:
  - Input: 12,801 x 7 
  - Output: 12,801 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 4,493 rows retrieved.
4493
WARNING: In order to set gene_output='rownames' must set drop_nonorths=TRUE.
 Setting drop_nonorths=TRUE.
WARNING: In order to set gene_output='rownames' must ensure unqiue rownmaes by setting non121_strategy to:
   'drop_both_species' or 'keep_popular' 
 or an aggregation function:
    'sum','mean','median','min','max' .
 Setting non121_strategy='drop_both_species'.
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.
Dropping 56 genes that have multiple ortholog_gene per input_gene.
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.
Dropping 56 genes that have multiple ortholog_gene per input_gene.
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.
Dropping 56 genes that have multiple ortholog_gene per input_gene.
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.
Dropping 56 genes that have multiple ortholog_gene per input_gene.
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.
14,192 genes extracted.
15,259 / 14,192 (93.01%) 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
Adding input_gene col to gene_df.
Adding input_gene_standard col to gene_df.
Adding ortholog_gene col to gene_df.
Sorting rownames alphanumerically.

=========== REPORT SUMMARY ===========

Total genes dropped after convert_orthologs :
   2,703 / 15,259 (18%)
Total genes remaining after convert_orthologs :
   12,556 / 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.
12,556 genes extracted.
Extracting genes from ortholog_gene.
12,556 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 30 genes that have multiple ortholog_gene per input_gene.
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 / 12,556 (0.41%)
Total genes remaining after convert_orthologs :
   12,504 / 12,556 (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.
Dropping 56 genes that have multiple ortholog_gene per input_gene.
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.
Dropping 56 genes that have multiple ortholog_gene per input_gene.
Filtering gene_df with gene_map
nrow(gene_map) > nrow(gene_df)
Checking for genes without 1:1 orthologs.
Extracting genes from input_gene.
13,320 genes extracted.
Extracting genes from input_gene.
13,320 genes extracted.
gene_map has the same number of rows as gene_df, 
                 and thus there is nothing to aggregate.
 Returning gene_df with gene names from gene_map instead
Aggregating rows using: monocle3
Matrix aggregated:
  - Input: 13,320 x 7 
  - Output: 13,320 x 7
Converting obj to sparseMatrix.

=========== REPORT SUMMARY ===========

Total genes dropped after convert_orthologs :
   1,939 / 15,259 (13%)
Total genes remaining after convert_orthologs :
   13,320 / 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 9,398 genes that have multiple input_gene per ortholog_gene.
Dropping 10,409 genes that have multiple ortholog_gene per input_gene.
Filtering gene_df with gene_map
Setting ortholog_gene to rownames.

=========== REPORT SUMMARY ===========

Total genes dropped after convert_orthologs :
   4,034 / 15,259 (26%)
Total genes remaining after convert_orthologs :
   11,225 / 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
Checking for genes without orthologs in mouse.
Extracting genes from input_gene.
15,335 genes extracted.
Extracting genes from ortholog_gene.
15,335 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 1,342 genes that have multiple input_gene per ortholog_gene.
Dropping 807 genes that have multiple ortholog_gene per input_gene.
Filtering gene_df with gene_map
Setting ortholog_gene to rownames.
Converting obj to sparseMatrix.

=========== REPORT SUMMARY ===========

Total genes dropped after convert_orthologs :
   1,545 / 15,259 (10%)
Total genes remaining after convert_orthologs :
   13,714 / 15,259 (90%)
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.
Dropping 56 genes that have multiple ortholog_gene per input_gene.
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
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: 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.
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.
Dropping 498 genes that have multiple ortholog_gene per input_gene.
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.
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.
--
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.
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.
Dropping 607 genes that have multiple ortholog_gene per input_gene.
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
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: 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.
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.
Dropping 1,975 genes that have multiple ortholog_gene per input_gene.
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.
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.
Generating gene background for human x rat ==> mouse
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.
--
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.
Dropping 131 genes that have multiple ortholog_gene per input_gene.
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.
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.
--
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.
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.
Dropping 2,075 genes that have multiple ortholog_gene per input_gene.
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
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.
--
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.
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 203 genes that have multiple input_gene per ortholog_gene.
Dropping 221 genes that have multiple ortholog_gene per input_gene.
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 :
   1,730 / 16,816 (10%)
Total genes remaining after convert_orthologs :
   15,086 / 16,816 (90%)
--

=========== REPORT SUMMARY ===========

15,075 / 16,816 (89.65%) target_species genes remain after ortholog conversion.
15,075 / 19,129 (78.81%) reference_species genes remain after ortholog conversion.
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.
--
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.
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 281 genes that have multiple input_gene per ortholog_gene.
Dropping 175 genes that have multiple ortholog_gene per input_gene.
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 :
   1,511 / 18,703 (8.1%)
Total genes remaining after convert_orthologs :
   17,192 / 18,703 (92%)
--

=========== REPORT SUMMARY ===========

17,183 / 18,703 (91.87%) target_species genes remain after ortholog conversion.
17,183 / 19,129 (89.83%) reference_species genes remain after ortholog conversion.
14,187 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%
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.
9 / 3 (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.
9 / 7 (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.
9 / 3 (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.
71 genes extracted.
1,000 / 71 (7.1%) 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
input_species==output_species. Returning input genes.
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.

-- 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.

-- 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.
--
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.
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 203 genes that have multiple input_gene per ortholog_gene.
Dropping 221 genes that have multiple ortholog_gene per input_gene.
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 :
   1,730 / 16,816 (10%)
Total genes remaining after convert_orthologs :
   15,086 / 16,816 (90%)
--

=========== REPORT SUMMARY ===========

15,075 / 16,816 (89.65%) target_species genes remain after ortholog conversion.
15,075 / 19,129 (78.81%) 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.
--
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.
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.
Dropping 498 genes that have multiple ortholog_gene per input_gene.
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
***************************************************************
*                          Note:                              *
*    force.ultrametric does not include a formal method to    *
*    ultrametricize a tree & should only be used to coerce    *
*   a phylogeny that fails is.ultramtric due to rounding --   *
*    not as a substitute for formal rate-smoothing methods.   *
***************************************************************
Mapping 3 species from `species`.
Mapping 100 species from tree.
--
91/100 (91%) tips dropped from tree due to inability to standardise names with `map_species`.
--
6/9 (67%) tips dropped from tree according to overlap with selected `species`.
Loading required namespace: rphylopic
Gathering phylopic silhouettes.
Homo sapiens
try:  1
Macaca mulatta
try:  1
Mus musculus
try:  1
Preparing data for 5 clades.
3 species remaining after metadata preparation.
Loading required namespace: ggimage
Loading required namespace: RColorBrewer
Creating ggtree plot.
Saving plot ==> F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpYdGzq4\file22a4965734.ggtree.pdf
Saving plot ==> F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpYdGzq4\file22a44cbb745c.ggtree.png
Gathering ortholog reports.

-- 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.

-- 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.
--
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.
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
20,402 genes extracted.
Converting monkey ==> human 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: 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: 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 human.
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 1,586 genes that have multiple input_gene per ortholog_gene.
Dropping 1,215 genes that have multiple ortholog_gene per input_gene.
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 :
   1,756 / 18,149 (9.7%)
Total genes remaining after convert_orthologs :
   16,393 / 18,149 (90%)
--

=========== REPORT SUMMARY ===========

16,315 / 18,149 (89.89%) target_species genes remain after ortholog conversion.
16,315 / 20,206 (80.74%) 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.
--
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.
--
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 9,398 genes that have multiple input_gene per ortholog_gene.
Dropping 10,409 genes that have multiple ortholog_gene per input_gene.
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 :
   4,717 / 20,075 (23%)
Total genes remaining after convert_orthologs :
   15,358 / 20,075 (77%)
--

=========== REPORT SUMMARY ===========

15,271 / 20,075 (76.07%) target_species genes remain after ortholog conversion.
15,271 / 20,206 (75.58%) reference_species genes remain after ortholog conversion.
***************************************************************
*                          Note:                              *
*    force.ultrametric does not include a formal method to    *
*    ultrametricize a tree & should only be used to coerce    *
*   a phylogeny that fails is.ultramtric due to rounding --   *
*    not as a substitute for formal rate-smoothing methods.   *
***************************************************************
Mapping 3 species from `species`.
Mapping 100 species from tree.
--
84/100 (84%) tips dropped from tree due to inability to standardise names with `map_species`.
--
13/16 (81%) tips dropped from tree according to overlap with selected `species`.
Gathering phylopic silhouettes.
Homo sapiens
try:  1
Macaca mulatta
try:  1
Mus musculus
try:  1
Preparing data for 5 clades.
3 species remaining after metadata preparation.
Creating ggtree plot.
Saving plot ==> F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpYdGzq4\file22a4c4a2d72.ggtree.pdf
Saving plot ==> F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpYdGzq4\file22a4710658b7.ggtree.png
***************************************************************
*                          Note:                              *
*    force.ultrametric does not include a formal method to    *
*    ultrametricize a tree & should only be used to coerce    *
*   a phylogeny that fails is.ultramtric due to rounding --   *
*    not as a substitute for formal rate-smoothing methods.   *
***************************************************************
Mapping 3 species from `species`.
Mapping 100 species from tree.
--
29/100 (29%) tips dropped from tree due to inability to standardise names with `map_species`.
--
68/71 (96%) tips dropped from tree according to overlap with selected `species`.
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: 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.
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.
Dropping 498 genes that have multiple ortholog_gene per input_gene.
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.
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: 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.
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 47 genes that have multiple input_gene per ortholog_gene.
Dropping 2,708 genes that have multiple ortholog_gene per input_gene.
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 :
   10,338 / 20,895 (49%)
Total genes remaining after convert_orthologs :
   10,557 / 20,895 (51%)
--

=========== REPORT SUMMARY ===========

10,556 / 20,895 (50.52%) target_species genes remain after ortholog conversion.
10,556 / 19,129 (55.18%) reference_species genes remain after ortholog conversion.
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: 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.
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.
Dropping 266 genes that have multiple ortholog_gene per input_gene.
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.
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.
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.
--
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.
--
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 9,398 genes that have multiple input_gene per ortholog_gene.
Dropping 10,409 genes that have multiple ortholog_gene per input_gene.
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 :
   4,717 / 20,075 (23%)
Total genes remaining after convert_orthologs :
   15,358 / 20,075 (77%)
--

=========== REPORT SUMMARY ===========

15,271 / 20,075 (76.07%) target_species genes remain after ortholog conversion.
15,271 / 20,206 (75.58%) reference_species genes remain after ortholog conversion.
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 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.
--
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 11,026 genes that have multiple input_gene per ortholog_gene.
Dropping 14,624 genes that have multiple ortholog_gene per input_gene.
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 :
   11,934 / 19,781 (60%)
Total genes remaining after convert_orthologs :
   7,847 / 19,781 (40%)
--

=========== REPORT SUMMARY ===========

7,805 / 19,781 (39.46%) target_species genes remain after ortholog conversion.
7,805 / 20,206 (38.63%) reference_species genes remain after ortholog conversion.
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.
--
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.
--
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 11,729 genes that have multiple input_gene per ortholog_gene.
Dropping 9,149 genes that have multiple ortholog_gene per input_gene.
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 :
   5,181 / 8,471 (61%)
Total genes remaining after convert_orthologs :
   3,290 / 8,471 (39%)
--

=========== REPORT SUMMARY ===========

3,273 / 8,471 (38.64%) target_species genes remain after ortholog conversion.
3,273 / 20,206 (16.2%) reference_species genes remain after ortholog conversion.
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.

-- 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.
--
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.
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.
Dropping 498 genes that have multiple ortholog_gene per input_gene.
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.
--
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.
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 203 genes that have multiple input_gene per ortholog_gene.
Dropping 221 genes that have multiple ortholog_gene per input_gene.
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 :
   1,730 / 16,816 (10%)
Total genes remaining after convert_orthologs :
   15,086 / 16,816 (90%)
--

=========== REPORT SUMMARY ===========

15,075 / 16,816 (89.65%) target_species genes remain after ortholog conversion.
15,075 / 19,129 (78.81%) 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.
Dropping 266 genes that have multiple ortholog_gene per input_gene.
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 4,493 rows retrieved.
Extracting genes from Gene.Symbol.
4,493 genes extracted.
Dropping 1 NAs of all kinds from Gene.Symbol.
Returning all 4,492 genes from fruit fly.
Benchmarking convert_orthologs()
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
4,492 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.
6,467 genes extracted.
Extracting genes from ortholog_gene.
6,467 genes extracted.
Dropping 3,409 NAs of all kinds from ortholog_gene.
Checking for genes without 1:1 orthologs.
Dropping 1,911 genes that have multiple input_gene per ortholog_gene.
Dropping 751 genes that have multiple ortholog_gene per input_gene.
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 :
   3,845 / 4,492 (86%)
Total genes remaining after convert_orthologs :
   647 / 4,492 (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 11,729 genes that have multiple input_gene per ortholog_gene.
Dropping 9,149 genes that have multiple ortholog_gene per input_gene.
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 :
   5,179 / 8,469 (61%)
Total genes remaining after convert_orthologs :
   3,290 / 8,469 (39%)
Finished fruit fly in 0.209 minutes.
Saving benchmarking results ==> F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpYdGzq4\file22a47bcc34b0.csv
WARNING: Species 'monkeytypo' not found in taxa dict.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 145 ]
> 
> proc.time()
   user  system elapsed 
 217.26    5.25  302.31