Type: Package
Title: Gene Orthologs for Model Organisms in a Tidy Data Format
Version: 22.9
Description: Genomic analysis of model organisms frequently requires the use of databases based on human data or making comparisons to patient-derived resources. This requires harmonization of gene names into the same gene space. The 'babelgene' R package converts between human and non-human gene orthologs/homologs. The package integrates orthology assertion predictions sourced from multiple databases as compiled by the HGNC Comparison of Orthology Predictions (HCOP) (Wright et al. 2005 <doi:10.1007/s00335-005-0103-2>, Eyre et al. 2007 <doi:10.1093/bib/bbl030>, Seal et al. 2011 <doi:10.1093/nar/gkq892>).
License: MIT + file LICENSE
URL: https://igordot.github.io/babelgene/
BugReports: https://github.com/igordot/babelgene/issues
Depends: R (≥ 3.4)
Imports: dplyr, methods, rlang
Suggests: covr, knitr, rmarkdown, testthat (≥ 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
Encoding: UTF-8
RoxygenNote: 7.2.1
NeedsCompilation: no
Packaged: 2022-09-28 16:45:01 UTC; id460
Author: Igor Dolgalev ORCID iD [aut, cre]
Maintainer: Igor Dolgalev <igor.dolgalev@nyumc.org>
Repository: CRAN
Date/Publication: 2022-09-29 09:40:17 UTC

Retrieve gene orthologs/homologs

Description

Retrieve gene orthologs/homologs for a set of genes. Converts between human and non-human analogs.

Usage

orthologs(genes, species, human = TRUE, min_support = 3, top = TRUE)

Arguments

genes

A vector of gene symbols or Entrez/Ensembl IDs.

species

Species name, such as Mus musculus or mouse (see species() for options).

human

A logical scalar indicating if the input genes are human. If TRUE, the input genes are human. If FALSE, the input genes correspond to the non-human species and the output will be the human equivalents.

min_support

Minimum number of supporting source databases. Gene pairs available in this package are supported by 2 to 12 databases (the maximum varies depending on the species).

top

For each gene, output only the match with the highest support level if there are multiple hits.

Value

A data frame of gene pairs (human and given species).

References

Wright MW, Eyre TA, Lush MJ, Povey S, Bruford EA. HCOP: the HGNC comparison of orthology predictions search tool. Mamm Genome. 2005 Nov;16(11):827-8. doi:10.1007/s00335-005-0103-2

Eyre TA, Wright MW, Lush MJ, Bruford EA. HCOP: a searchable database of human orthology predictions. Brief Bioinform. 2007 Jan;8(1):2-5. doi:10.1093/bib/bbl030

Seal RL, Gordon SM, Lush MJ, Wright MW, Bruford EA. genenames.org: the HGNC resources in 2011. Nucleic Acids Res. 2011 Jan;39:D514-9. doi:10.1093/nar/gkq892

Examples

orthologs(genes = "TP53", species = "mouse", human = TRUE)
orthologs(genes = c("Ptprc", "Cd34"), species = "mouse", human = FALSE)

Retrieve the available species

Description

List the species with available human orthologs.

Usage

species(species = NULL)

Arguments

species

Species name, such as Mus musculus or mouse. If specified, will return results for the given species only.

Value

A data frame of the available species.

Examples

species()
species("Mus musculus")
species("mouse")
species("rat")