convert_gene_symbols_species: Convert gene identifiers from mouse to human or human to...

In mjdufort/RNAseQC: Helper functions for conducting quality control of RNAseq data

Convert gene identifiers from mouse to human or human to mouse, using orthologs

Description

Convert a vector of symbols from one species to another. Current options exist only for mouse to human and identifiers from one standard to another. Mouse identifiers will be MGI symbols. Human identifiers will be HGNC symbols. Multiple genes may be returned for any input gene, based on the possible one-to-many mapping of gene orthologs. This function is adapted from https://www.biostars.org/p/9567892/, and uses the MGI list of orthologs at https://www.informatics.jax.org/downloads/reports/HOM_MouseHumanSequence.rpt

Usage

convert_gene_symbols_species(
  genes,
  species_from,
  species_to,
  return_format = "orthologs_only"
)

Arguments

genes	character vector containing gene identifiers to convert
species_from	character, the species of the input gene identifiers. Must be "mouse" or "human"; partial matches are accepted.
species_to	character, the species of the output gene identifiers. Must be "mouse" or "human"; partial matches are accepted.
return_format	character, the format of the output gene identifiers. Must be "orthologs_only" or "orig_and_ortholog"; partial matches are accepted.

Value

a vector of gene symbols, of length similar to the input genes, minus any genes that do not have orthologs in 'species_to'.

mjdufort/RNAseQC documentation built on Dec. 12, 2024, 2:58 p.m.