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Retrieve gene orthologs/homologs

Source: R/functions.R
orthologs.Rd

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)
#>   human_symbol human_entrez   human_ensembl taxon_id symbol entrez
#> 1         TP53         7157 ENSG00000141510    10090  Trp53  22059
#>              ensembl
#> 1 ENSMUSG00000059552
#>                                                                                         support
#> 1 EggNOG|Ensembl|HGNC|HomoloGene|Inparanoid|NCBI|OMA|OrthoDB|OrthoMCL|Panther|PhylomeDB|Treefam
#>   support_n
#> 1        12
orthologs(genes = c("Ptprc", "Cd34"), species = "mouse", human = FALSE)
#>   human_symbol human_entrez   human_ensembl taxon_id symbol entrez
#> 1         CD34          947 ENSG00000174059    10090   Cd34  12490
#> 2        PTPRC         5788 ENSG00000081237    10090  Ptprc  19264
#>              ensembl
#> 1 ENSMUSG00000016494
#> 2 ENSMUSG00000026395
#>                                                                                         support
#> 1 EggNOG|Ensembl|HGNC|HomoloGene|Inparanoid|NCBI|OMA|OrthoDB|OrthoMCL|Panther|PhylomeDB|Treefam
#> 2                   EggNOG|Ensembl|HGNC|HomoloGene|Inparanoid|NCBI|OMA|OrthoDB|OrthoMCL|Panther
#>   support_n
#> 1        12
#> 2        10