Convert gene symbols to Entrez IDs

Usage

gene2entrez(x, ref = NULL, species = c("human", "mouse"))

Arguments

x: Character vector of gene symbols.
ref: Data frame with columns symbol and entrez_id. If NULL (default), a full reference is downloaded via download_gene_ref — this may trigger a network request. For examples and tests, pass toy_gene_ref() instead.
species: One of "human" or "mouse". Controls symbol case normalization before matching. Default: "human".

Value

A data.frame with columns symbol (original input), symbol_std (case-normalized), and entrez_id. Unmatched entries have NA in entrez_id.

Examples

ref <- toy_gene_ref(species = "human")
gene2entrez(c("tp53", "brca1", "MYC"), ref = ref, species = "human")
#>   symbol symbol_std entrez_id
#> 1   tp53       TP53        NA
#> 2  brca1      BRCA1        NA
#> 3    MYC        MYC        NA

ref <- toy_gene_ref(species = "mouse")
gene2entrez(c("Trp53", "Zbp1"), ref = ref, species = "mouse")
#>   symbol symbol_std entrez_id
#> 1  Trp53      trp53        NA
#> 2   Zbp1       zbp1     58203