Installation

if (!requireNamespace("BiocManager", quietly = TRUE))
     install.packages("BiocManager") 
# orthogene is only available on Bioconductor>=3.14
if(BiocManager::version()<"3.14") 
  BiocManager::install(update = TRUE, ask = FALSE)

BiocManager::install("orthogene")

library(orthogene)

data("exp_mouse")
# Setting to "homologene" for the purposes of quick demonstration.
# We generally recommend using method="gprofiler" (default).
method <- "homologene"

Introduction

It’s not always clear whether a dataset is using the original species gene names, human gene names, or some other species’ gene names.

infer_species takes a list/matrix/data.frame with genes and infers the species that they best match to!

For the sake of speed, the genes extracted from gene_df are tested against genomes from only the following 6 test_species by default: - human - monkey - rat - mouse - zebrafish - fly

However, you can supply your own list of test_species, which will be automatically be mapped and standardised using map_species.

Examples

Mouse genes

Infer the species

matches <- orthogene::infer_species(gene_df = exp_mouse, 
                                    method = method)

## Preparing gene_df.

## sparseMatrix format detected.

## Extracting genes from rownames.

## 15,259 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: 92%

Rat genes

Create example data

To create an example dataset, turn the gene names into rat genes.

exp_rat <- orthogene::convert_orthologs(gene_df = exp_mouse, 
                                        input_species = "mouse", 
                                        output_species = "rat",
                                        method = method)

## Preparing gene_df.

## sparseMatrix format detected.

## Extracting genes from rownames.

## 15,259 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.

## 13,812 genes extracted.

## Extracting genes from ortholog_gene.

## 13,812 genes extracted.

## Checking for genes without 1:1 orthologs.

## Dropping 486 genes that have multiple input_gene per ortholog_gene (many:1).

## Dropping 148 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 :
##    2,322 / 15,259 (15%)

## Total genes remaining after convert_orthologs :
##    12,937 / 15,259 (85%)

Infer the species

matches <- orthogene::infer_species(gene_df = exp_rat, 
                                    method = method)

## Preparing gene_df.

## sparseMatrix format detected.

## Extracting genes from rownames.

## 12,937 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: rat 
##   - percent_match: 100%

Human genes

Create example data

To create an example dataset, turn the gene names into human genes.

exp_human <- orthogene::convert_orthologs(gene_df = exp_mouse, 
                                          input_species = "mouse", 
                                          output_species = "human",
                                          method = method)

## 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.

## 
## =========== REPORT SUMMARY ===========

## Total genes dropped after convert_orthologs :
##    2,016 / 15,259 (13%)

## Total genes remaining after convert_orthologs :
##    13,243 / 15,259 (87%)

Infer the species

matches <- orthogene::infer_species(gene_df = exp_human, 
                                    method = method)

## Preparing gene_df.

## sparseMatrix format detected.

## Extracting genes from rownames.

## 13,243 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: 100%

Additional `test_species`

You can even supply test_species with the name of one of the R packages that orthogene gets orthologs from. This will test against all species available in that particular R package.

For example, by setting test_species="homologene" we automatically test for % gene matches in each of the 20+ species available in homologene.

matches <- orthogene::infer_species(gene_df = exp_human, 
                                    test_species = method, 
                                    method = method)

## Retrieving all organisms available in homologene.

## Preparing gene_df.

## sparseMatrix format detected.

## Extracting genes from rownames.

## 13,243 genes extracted.

## Testing for gene overlap with: Mus musculus

## Retrieving all genes using: homologene.

## Retrieving all organisms available in homologene.

## Mapping species name: Mus musculus

## 1 organism identified from search: 10090

## Gene table with 21,207 rows retrieved.

## Returning all 21,207 genes from Mus musculus.

## Testing for gene overlap with: Rattus norvegicus

## Retrieving all genes using: homologene.

## Retrieving all organisms available in homologene.

## Mapping species name: Rattus norvegicus

## 1 organism identified from search: 10116

## Gene table with 20,616 rows retrieved.

## Returning all 20,616 genes from Rattus norvegicus.

## Testing for gene overlap with: Kluyveromyces lactis

## Retrieving all genes using: homologene.

## Retrieving all organisms available in homologene.

## Mapping species name: Kluyveromyces lactis

## 1 organism identified from search: 28985

## Gene table with 4,283 rows retrieved.

## Returning all 4,283 genes from Kluyveromyces lactis.

## Testing for gene overlap with: Magnaporthe oryzae

## Retrieving all genes using: homologene.

## Retrieving all organisms available in homologene.

## Mapping species name: Magnaporthe oryzae

## 1 organism identified from search: 318829

## Gene table with 6,598 rows retrieved.

## Returning all 6,598 genes from Magnaporthe oryzae.

## Testing for gene overlap with: Eremothecium gossypii

## Retrieving all genes using: homologene.

## Retrieving all organisms available in homologene.

## Mapping species name: Eremothecium gossypii

## 1 organism identified from search: 33169

## Gene table with 3,874 rows retrieved.

## Returning all 3,874 genes from Eremothecium gossypii.

## Testing for gene overlap with: Arabidopsis thaliana

## Retrieving all genes using: homologene.

## Retrieving all organisms available in homologene.

## Mapping species name: Arabidopsis thaliana

## 1 organism identified from search: 3702

## Gene table with 19,143 rows retrieved.

## Returning all 19,143 genes from Arabidopsis thaliana.

## Testing for gene overlap with: Oryza sativa

## Retrieving all genes using: homologene.

## Retrieving all organisms available in homologene.

## Mapping species name: Oryza sativa

## 1 organism identified from search: 4530

## Gene table with 16,112 rows retrieved.

## Returning all 16,112 genes from Oryza sativa.

## Testing for gene overlap with: Schizosaccharomyces pombe

## Retrieving all genes using: homologene.

## Retrieving all organisms available in homologene.

## Mapping species name: Schizosaccharomyces pombe

## 1 organism identified from search: 4896

## Gene table with 3,018 rows retrieved.

## Returning all 3,018 genes from Schizosaccharomyces pombe.

## Testing for gene overlap with: Saccharomyces cerevisiae

## Retrieving all genes using: homologene.

## Retrieving all organisms available in homologene.

## Mapping species name: Saccharomyces cerevisiae

## 1 organism identified from search: 4932

## Gene table with 4,579 rows retrieved.

## Returning all 4,579 genes from Saccharomyces cerevisiae.

## Testing for gene overlap with: Neurospora crassa

## Retrieving all genes using: homologene.

## Retrieving all organisms available in homologene.

## Mapping species name: Neurospora crassa

## 1 organism identified from search: 5141

## Gene table with 5,807 rows retrieved.

## Returning all 5,807 genes from Neurospora crassa.

## Testing for gene overlap with: Caenorhabditis elegans

## Retrieving all genes using: homologene.

## Retrieving all organisms available in homologene.

## Mapping species name: Caenorhabditis elegans

## 1 organism identified from search: 6239

## Gene table with 7,575 rows retrieved.

## Returning all 7,575 genes from Caenorhabditis elegans.

## Testing for gene overlap with: Anopheles gambiae

## Retrieving all genes using: homologene.

## Retrieving all organisms available in homologene.

## Mapping species name: Anopheles gambiae

## 1 organism identified from search: 7165

## Gene table with 8,428 rows retrieved.

## Returning all 8,428 genes from Anopheles gambiae.

## Testing for gene overlap with: Drosophila melanogaster

## Retrieving all genes using: homologene.

## Retrieving all organisms available in homologene.

## Mapping species name: Drosophila melanogaster

## 1 organism identified from search: 7227

## Gene table with 8,438 rows retrieved.

## Returning all 8,438 genes from Drosophila melanogaster.

## Testing for gene overlap with: Danio rerio

## Retrieving all genes using: homologene.

## Retrieving all organisms available in homologene.

## Mapping species name: Danio rerio

## 1 organism identified from search: 7955

## Gene table with 20,897 rows retrieved.

## Returning all 20,897 genes from Danio rerio.

## Testing for gene overlap with: Xenopus (Silurana) tropicalis

## Retrieving all genes using: homologene.

## Retrieving all organisms available in homologene.

## Mapping species name: Xenopus (Silurana) tropicalis

## 1 organism identified from search: 8364

## Gene table with 18,446 rows retrieved.

## Returning all 18,446 genes from Xenopus (Silurana) tropicalis.

## Testing for gene overlap with: Gallus gallus

## Retrieving all genes using: homologene.

## Retrieving all organisms available in homologene.

## Mapping species name: Gallus gallus

## 1 organism identified from search: 9031

## Gene table with 14,600 rows retrieved.

## Returning all 14,600 genes from Gallus gallus.

## Testing for gene overlap with: Macaca mulatta

## Retrieving all genes using: homologene.

## Retrieving all organisms available in homologene.

## Mapping species name: Macaca mulatta

## 1 organism identified from search: 9544

## Gene table with 16,843 rows retrieved.

## Returning all 16,843 genes from Macaca mulatta.

## Testing for gene overlap with: Pan troglodytes

## Retrieving all genes using: homologene.

## Retrieving all organisms available in homologene.

## Mapping species name: Pan troglodytes

## 1 organism identified from search: 9598

## Gene table with 18,730 rows retrieved.

## Returning all 18,730 genes from Pan troglodytes.

## Testing for gene overlap with: Homo sapiens

## 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.

## Testing for gene overlap with: Canis lupus familiaris

## Retrieving all genes using: homologene.

## Retrieving all organisms available in homologene.

## Mapping species name: Canis lupus familiaris

## 1 organism identified from search: 9615

## Gene table with 18,117 rows retrieved.

## Returning all 18,117 genes from Canis lupus familiaris.

## Testing for gene overlap with: Bos taurus

## Retrieving all genes using: homologene.

## Retrieving all organisms available in homologene.

## Mapping species name: Bos taurus

## 1 organism identified from search: 9913

## Gene table with 18,797 rows retrieved.

## Returning all 18,797 genes from Bos taurus.

## Top match:
##   - species: Homo sapiens 
##   - percent_match: 100%

Session Info

utils::sessionInfo()

## R version 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: Etc/UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] orthogene_1.13.0 BiocStyle_2.35.0
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.6              babelgene_22.9           
##  [3] xfun_0.49                 bslib_0.8.0              
##  [5] ggplot2_3.5.1             htmlwidgets_1.6.4        
##  [7] rstatix_0.7.2             lattice_0.22-6           
##  [9] vctrs_0.6.5               tools_4.4.2              
## [11] generics_0.1.3            yulab.utils_0.1.8        
## [13] parallel_4.4.2            tibble_3.2.1             
## [15] fansi_1.0.6               pkgconfig_2.0.3          
## [17] Matrix_1.7-1              data.table_1.16.2        
## [19] homologene_1.4.68.19.3.27 ggplotify_0.1.2          
## [21] lifecycle_1.0.4           compiler_4.4.2           
## [23] farver_2.1.2              treeio_1.31.0            
## [25] munsell_0.5.1             carData_3.0-5            
## [27] ggtree_3.15.0             gprofiler2_0.2.3         
## [29] ggfun_0.1.7               htmltools_0.5.8.1        
## [31] sys_3.4.3                 buildtools_1.0.0         
## [33] sass_0.4.9                yaml_2.3.10              
## [35] lazyeval_0.2.2            plotly_4.10.4            
## [37] Formula_1.2-5             pillar_1.9.0             
## [39] car_3.1-3                 ggpubr_0.6.0             
## [41] jquerylib_0.1.4           tidyr_1.3.1              
## [43] cachem_1.1.0              grr_0.9.5                
## [45] abind_1.4-8               nlme_3.1-166             
## [47] tidyselect_1.2.1          aplot_0.2.3              
## [49] digest_0.6.37             dplyr_1.1.4              
## [51] purrr_1.0.2               labeling_0.4.3           
## [53] maketools_1.3.1           fastmap_1.2.0            
## [55] grid_4.4.2                colorspace_2.1-1         
## [57] cli_3.6.3                 magrittr_2.0.3           
## [59] patchwork_1.3.0           utf8_1.2.4               
## [61] broom_1.0.7               ape_5.8                  
## [63] withr_3.0.2               scales_1.3.0             
## [65] backports_1.5.0           httr_1.4.7               
## [67] rmarkdown_2.29            ggsignif_0.6.4           
## [69] evaluate_1.0.1            knitr_1.49               
## [71] viridisLite_0.4.2         gridGraphics_0.5-1       
## [73] rlang_1.1.4               Rcpp_1.0.13-1            
## [75] glue_1.8.0                tidytree_0.4.6           
## [77] BiocManager_1.30.25       jsonlite_1.8.9           
## [79] R6_2.5.1                  fs_1.6.5

Infer species

Installation

Introduction

Examples

Mouse genes

Infer the species

Rat genes

Create example data

Infer the species

Human genes

Create example data

Infer the species

Additional test_species

Session Info

Additional `test_species`