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
## 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%

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)
## 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.
## Dropping 148 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 :
##    2,322 / 15,259 (15%)
## Total genes remaining after convert_orthologs :
##    12,937 / 15,259 (85%)

3.2.2 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%

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)
## 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.
## 
## =========== REPORT SUMMARY ===========
## Total genes dropped after convert_orthologs :
##    2,016 / 15,259 (13%)
## Total genes remaining after convert_orthologs :
##    13,243 / 15,259 (87%)

3.3.2 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%

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)
## 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%

5 Session Info

utils::sessionInfo()
## R version 4.2.0 RC (2022-04-19 r82224)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.15-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.15-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              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       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] orthogene_1.2.0  BiocStyle_2.24.0
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.8.3              ape_5.6-2                
##  [3] lattice_0.20-45           tidyr_1.2.0              
##  [5] assertthat_0.2.1          digest_0.6.29            
##  [7] utf8_1.2.2                R6_2.5.1                 
##  [9] backports_1.4.1           evaluate_0.15            
## [11] highr_0.9                 httr_1.4.2               
## [13] ggplot2_3.3.5             pillar_1.7.0             
## [15] ggfun_0.0.6               yulab.utils_0.0.4        
## [17] rlang_1.0.2               lazyeval_0.2.2           
## [19] data.table_1.14.2         car_3.0-12               
## [21] jquerylib_0.1.4           magick_2.7.3             
## [23] Matrix_1.4-1              rmarkdown_2.14           
## [25] labeling_0.4.2            stringr_1.4.0            
## [27] htmlwidgets_1.5.4         munsell_0.5.0            
## [29] broom_0.8.0               gprofiler2_0.2.1         
## [31] compiler_4.2.0            xfun_0.30                
## [33] pkgconfig_2.0.3           gridGraphics_0.5-1       
## [35] htmltools_0.5.2           tidyselect_1.1.2         
## [37] tibble_3.1.6              bookdown_0.26            
## [39] viridisLite_0.4.0         fansi_1.0.3              
## [41] crayon_1.5.1              dplyr_1.0.8              
## [43] ggpubr_0.4.0              grid_4.2.0               
## [45] nlme_3.1-157              jsonlite_1.8.0           
## [47] gtable_0.3.0              lifecycle_1.0.1          
## [49] DBI_1.1.2                 magrittr_2.0.3           
## [51] scales_1.2.0              tidytree_0.3.9           
## [53] cli_3.3.0                 stringi_1.7.6            
## [55] carData_3.0-5             farver_2.1.0             
## [57] ggsignif_0.6.3            ggtree_3.4.0             
## [59] bslib_0.3.1               ellipsis_0.3.2           
## [61] generics_0.1.2            vctrs_0.4.1              
## [63] treeio_1.20.0             tools_4.2.0              
## [65] homologene_1.4.68.19.3.27 ggplotify_0.1.0          
## [67] glue_1.6.2                purrr_0.3.4              
## [69] abind_1.4-5               parallel_4.2.0           
## [71] fastmap_1.1.0             yaml_2.3.5               
## [73] babelgene_22.3            colorspace_2.0-3         
## [75] BiocManager_1.30.17       rstatix_0.7.0            
## [77] aplot_0.1.3               plotly_4.10.0            
## [79] knitr_1.38                patchwork_1.1.1          
## [81] sass_0.4.1