| 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 
[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 |
human |
A logical scalar indicating if the input genes are human. If |
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 |
Value
A data frame of the available species.
Examples
species()
species("Mus musculus")
species("mouse")
species("rat")