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Convert Gene IDs Between Human and Mouse via Orthology

Source: R/convert_hm_orthologs.R
convert_hm_orthologs.Rd

Maps gene symbols or Ensembl IDs between human and mouse using Ensembl BioMart orthology data. This resolves homologous gene relationships (e.g., human TP53 <-> mouse Trp53).

Usage

convert_hm_orthologs(
  IDs,
  from_species = c("human", "mouse"),
  to_species = c("mouse", "human"),
  from_type = c("symbol", "ensembl"),
  to_type = c("symbol", "ensembl", "both"),
  multiple = FALSE,
  high_confidence_only = TRUE,
  mirrors = ENSEMBL_MIRRORS,
  cache_dir = getOption("IDConverter.datapath", tempdir()),
  verbose = TRUE
)

Arguments

IDs

a character vector of gene symbols or Ensembl IDs.

from_species

source species: "human" (default) or "mouse".

to_species

target species: "mouse" (default) or "human". Must differ from from_species.

from_type

type of input IDs: "symbol" (default) or "ensembl".

to_type

type of output IDs: "symbol" (default), "ensembl", or "both" to return both columns.

multiple

if TRUE, return a data.frame with all ortholog matches (e.g., one-to-many relationships).

high_confidence_only

if TRUE (default), restrict to orthologs with high confidence (confidence == 1) in Ensembl.

mirrors

character vector of Ensembl mirror URLs.

cache_dir

directory to cache query results. Set NULL to skip.

verbose

if TRUE, print progress messages.

Value

If multiple = FALSE, a character vector of converted IDs (NA for unmatched). If multiple = TRUE or to_type = "both", a data.frame.

Details

Requirements: This function requires the Bioconductor package biomaRt. Install it with:


if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("biomaRt")

Orthology data is queried live from Ensembl and cached locally.

Examples

# \donttest{
# Human symbol -> mouse symbol
convert_hm_orthologs(c("TP53", "KRAS", "EGFR"))
#> Querying Ensembl BioMart for human->mouse orthologs...
#>   Trying mirror: https://www.ensembl.org
#>     OK: 3 rows
#>   Cached to: /tmp/Rtmpu9e9wx/ortholog_human_to_mouse_symbol_symbol_hc.rda
#>    TP53    KRAS    EGFR 
#> "Trp53"  "Kras"  "Egfr" 

# Mouse symbol -> human symbol
convert_hm_orthologs(c("Trp53", "Kras"), from_species = "mouse", to_species = "human")
#> Querying Ensembl BioMart for mouse->human orthologs...
#>   Trying mirror: https://www.ensembl.org
#>     OK: 2 rows
#>   Cached to: /tmp/Rtmpu9e9wx/ortholog_mouse_to_human_symbol_symbol_hc.rda
#>  Trp53   Kras 
#> "TP53" "KRAS" 

# Human Ensembl -> mouse Ensembl
convert_hm_orthologs("ENSG00000141510", from_type = "ensembl", to_type = "ensembl")
#> Querying Ensembl BioMart for human->mouse orthologs...
#>   Trying mirror: https://www.ensembl.org
#>     OK: 1 rows
#>   Cached to: /tmp/Rtmpu9e9wx/ortholog_human_to_mouse_ensembl_ensembl_hc.rda
#>      ENSG00000141510 
#> "ENSMUSG00000059552" 
# }