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Convert Gene IDs between Ensembl and Hugo Symbol System

Source: R/common_human_and_mouse_ids.R
convert_hm_genes.Rd

Supports human (hg38, hg19, T2T), mouse (mm10, mm9), and worm (ce11, C. elegans) genomes.

Usage

convert_hm_genes(
  IDs,
  type = c("ensembl", "symbol"),
  genome_build = c("hg38", "hg19", "mm10", "mm9", "ce11", "T2T"),
  multiple = FALSE
)

Arguments

IDs

a character vector to convert.

type

type of input IDs, could be 'ensembl' or 'symbol'.

genome_build

reference genome build.

multiple

if TRUE, return a data.table instead of a string vector, so multiple identifier mappings can be kept.

Value

a vector or a data.table.

Note

This function matches against primary gene symbols only. For resolving outdated or alternative gene names (aliases like "MLL" -> "KMT2A"), use build_annotables() with include_synonyms = TRUE followed by resolve_gene_aliases().

See also

resolve_gene_aliases() for resolving gene symbol aliases.

Examples

# \donttest{
convert_hm_genes("ENSG00000243485")
#> Downloading https://zenodo.org/records/10360995/files/human_hg38_gene_info.rds to /tmp/Rtmpu9e9wx/human_hg38_gene_info.rds
#> [1] "MIR1302-2HG"
convert_hm_genes("ENSG00000243485", multiple = TRUE)
#>               from          to
#>             <char>      <char>
#> 1: ENSG00000243485 MIR1302-2HG
convert_hm_genes(c("TP53", "KRAS", "EGFR", "MYC"), type = "symbol")
#> [1] "ENSG00000141510" "ENSG00000133703" "ENSG00000146648" "ENSG00000136997"
# }