Contents

1 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"

2 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.

3 Examples

3.1 Mouse genes

3.1.1 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
## Using cached file: /Users/biocbuild/Library/Caches/org.R-project.R/R/orthogene/all_genes-9606-homologene.csv.gz
## 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.
## Caching file --> /Users/biocbuild/Library/Caches/org.R-project.R/R/orthogene/all_genes-9544-homologene.csv.gz
## 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.
## Caching file --> /Users/biocbuild/Library/Caches/org.R-project.R/R/orthogene/all_genes-10116-homologene.csv.gz
## 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
## Using cached file: /Users/biocbuild/Library/Caches/org.R-project.R/R/orthogene/all_genes-10090-homologene.csv.gz
## 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.
## Caching file --> /Users/biocbuild/Library/Caches/org.R-project.R/R/orthogene/all_genes-7955-homologene.csv.gz
## 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.
## Caching file --> /Users/biocbuild/Library/Caches/org.R-project.R/R/orthogene/all_genes-7227-homologene.csv.gz
## Returning all 8,438 genes from fly.
## Top match:
##   - species: mouse 
##   - percent_match: 92%

3.2 Rat genes

3.2.1 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)

3.2.2 Infer the species

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

3.3 Human genes

3.3.1 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)

3.3.2 Infer the species

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

4 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)

5 Session Info

utils::sessionInfo()
R Under development (unstable) (2025-11-04 r88984)
Platform: aarch64-apple-darwin20
Running under: macOS Ventura 13.7.8

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1

locale:
[1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] orthogene_1.17.2 BiocStyle_2.39.0

loaded via a namespace (and not attached):
 [1] ggiraph_0.9.2             tidyselect_1.2.1         
 [3] viridisLite_0.4.2         dplyr_1.1.4              
 [5] farver_2.1.2              R.utils_2.13.0           
 [7] S7_0.2.1                  fastmap_1.2.0            
 [9] lazyeval_0.2.2            homologene_1.4.68.19.3.27
[11] fontquiver_0.2.1          digest_0.6.39            
[13] lifecycle_1.0.4           tidytree_0.4.6           
[15] magrittr_2.0.4            compiler_4.6.0           
[17] rlang_1.1.6               sass_0.4.10              
[19] tools_4.6.0               yaml_2.3.12              
[21] data.table_1.17.8         knitr_1.51               
[23] ggsignif_0.6.4            labeling_0.4.3           
[25] htmlwidgets_1.6.4         RColorBrewer_1.1-3       
[27] aplot_0.2.9               abind_1.4-8              
[29] babelgene_22.9            withr_3.0.2              
[31] purrr_1.2.0               R.oo_1.27.1              
[33] grid_4.6.0                ggpubr_0.6.2             
[35] gdtools_0.4.4             ggplot2_4.0.1            
[37] scales_1.4.0              dichromat_2.0-0.1        
[39] tinytex_0.58              cli_3.6.5                
[41] rmarkdown_2.30            treeio_1.35.0            
[43] generics_0.1.4            otel_0.2.0               
[45] ggtree_4.1.1              httr_1.4.7               
[47] gprofiler2_0.2.4          ape_5.8-1                
[49] cachem_1.1.0              parallel_4.6.0           
[51] ggplotify_0.1.3           BiocManager_1.30.27      
[53] yulab.utils_0.2.3         vctrs_0.6.5              
[55] Matrix_1.7-4              jsonlite_2.0.0           
[57] fontBitstreamVera_0.1.1   carData_3.0-5            
[59] bookdown_0.46             car_3.1-3                
[61] gridGraphics_0.5-1        patchwork_1.3.2          
[63] rstatix_0.7.3             Formula_1.2-5            
[65] systemfonts_1.3.1         magick_2.9.0             
[67] plotly_4.11.0             tidyr_1.3.2              
[69] jquerylib_0.1.4           glue_1.8.0               
[71] gtable_0.3.6              tibble_3.3.0             
[73] pillar_1.11.1             rappdirs_0.3.3           
[75] htmltools_0.5.9           R6_2.6.1                 
[77] evaluate_1.0.5            lattice_0.22-7           
[79] R.methodsS3_1.8.2         backports_1.5.0          
[81] broom_1.0.11              ggfun_0.2.0              
[83] fontLiberation_0.1.0      bslib_0.9.0              
[85] Rcpp_1.1.0.8.2            nlme_3.1-168             
[87] xfun_0.55                 fs_1.6.6                 
[89] pkgconfig_2.0.3