Resolve Gene Symbol Aliases

Maps gene symbols through known aliases (synonyms) to their current official symbols and Ensembl gene IDs. This helps when working with outdated or alternative gene names (e.g., "MLL" -> "KMT2A").

Usage

resolve_gene_aliases(symbols, annotable, multiple = FALSE)

Arguments

symbols

a character vector of gene symbols to resolve.

annotable

a data.frame from build_annotables() with include_synonyms = TRUE. Must contain symbol and synonym columns.

multiple

if TRUE, return a data.frame with all matches (including cases where one alias maps to multiple genes).

Value

a data.frame (tibble) with columns:

query

the input gene symbols

symbol

resolved official gene symbol (NA if unmatched)

ensgene

resolved Ensembl gene ID (NA if unmatched)

When multiple = TRUE, each row is a single query->match pair, so one query may appear in multiple rows.

Examples

# \donttest{
# Build annotables with synonym support
ann <- build_annotables("grch38", include_synonyms = TRUE, tx2gene = FALSE)
#> --- Building: grch38 ---
#>   Trying mirror: https://www.ensembl.org
#>     OK: 133458 rows
#>   Cached to: /tmp/Rtmpu9e9wx/grch38_syn.rda
#> 
#> Successfully built 1 table(s). Use names() to see available tables.

# Resolve aliases
resolve_gene_aliases(c("TP53", "MLL", "NOTAGENE"), ann[[1]])
#> # A tibble: 3 × 3
#>   query    symbol ensgene        
#>   <chr>    <chr>  <chr>          
#> 1 TP53     TP53   ENSG00000141510
#> 2 MLL      KMT2A  ENSG00000118058
#> 3 NOTAGENE NA     NA             

# Multiple match mode
resolve_gene_aliases(c("TP53", "MLL"), ann[[1]], multiple = TRUE)
#> # A tibble: 2 × 3
#>   query symbol ensgene        
#>   <chr> <chr>  <chr>          
#> 1 TP53  TP53   ENSG00000141510
#> 2 MLL   KMT2A  ENSG00000118058
# }