Gene symbol matching — match_gene

Correct alias gene symbols, Ensembl IDs, and Entrez IDs to canonical gene symbols. This is useful for matching gene names between different datasets which might not always use the same gene naming conventions.

Usage

match_gene_symbol(query, subject, gene_mapping = human_gene_mapping)

canonical_gene_symbol(query, gene_mapping = human_gene_mapping)

Arguments

query: Character vector of gene symbols or IDs
subject: Vector of gene symbols or IDs to index into
gene_mapping: Named vector where names are gene symbols or IDs and values are canonical gene symbols

Value

match_gene_symbol

Integer vector of indices v such that subject[v] corresponds to the gene symbols in query

canonical_gene_symbol

Character vector of canonical gene symbols for each symbol in query

Examples

#######################################################################
## match_gene_symbol() example
#######################################################################
match_gene_symbol(
 c("CD8", "CD4", "CD45"),
 c("ENSG00000081237.19", "ENSG00000153563.15", "ENSG00000010610.9", "ENSG00000288825")
)
#> [1] 2 3 1


#######################################################################
## canonical_gene_symbol() example
#######################################################################
canonical_gene_symbol(c("CD45", "CD8", "CD4"))
#>    CD45     CD8     CD4 
#> "PTPRC"  "CD8A"   "CD4"