Package 'babelgene'

Title: Gene Orthologs for Model Organisms in a Tidy Data Format
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>).
Authors: Igor Dolgalev [aut, cre]
Maintainer: Igor Dolgalev <[email protected]>
License: MIT + file LICENSE
Version: 22.9
Built: 2024-08-25 05:26:02 UTC
Source: https://github.com/igordot/babelgene

Help Index

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")