Convert gene symbols between mouse and human — convert

Maps orthologous gene symbols between mouse (MGI) and human (HGNC) using Ensembl BioMart, or the Jackson Laboratory homology report as an alternative when the Ensembl servers are unreachable.

Usage

convert_mouse_to_human(genes, use.jax = FALSE, jax.table = NULL)

convert_human_to_mouse(genes, use.jax = FALSE, jax.table = NULL)

Arguments

genes: Character vector of gene symbols to convert.
use.jax: If TRUE, use the JAX HOM_MouseHumanSequence report instead of BioMart.
jax.table: Optional data frame holding the JAX report (as read by utils::read.delim()). If NULL the report is downloaded. Supplying it avoids the download and makes the conversion reproducible offline.

Value

With BioMart, a data frame with one row per ortholog pair (MGI.symbol, HGNC.symbol or the reverse). With use.jax = TRUE, a character vector of the converted symbols.

Details

Both directions keep one row per source symbol and per target symbol (the first match), so one-to-many orthologs are collapsed.

Examples

if (FALSE) { # \dontrun{
convert_mouse_to_human(c("Gzma", "Gzmb", "Xcl1"))
convert_human_to_mouse(c("GZMA", "GZMB", "XCL1"))
} # }