Parse variant IDs into a data frame

Converts variant IDs from any supported string format or data.frame into a standardized data.frame with a normalized character chrom, integer pos, and character allele columns (A2, A1). The chrom is canonicalized (chr stripped, uppercased, 23 -> X / 24 -> Y / M -> MT) but kept as a string so X/Y/MT survive. Supports colon-separated ("chr1:100:A:G"), underscore-separated ("1_100_A_G"), with or without "chr" prefix, and with optional build suffix (":b38" or "_b38"). The detected input convention is stored as an attribute.

Usage

parseVariantId(ids)

Arguments

ids

A character vector of variant IDs, or a data.frame with columns "chrom", "pos", and allele columns (A2/A1 or ref/alt or any 4-column layout).

Value

A tibble with columns "chrom" (character, normalized), "pos" (integer), "A2" (character), "A1" (character). The detected convention is stored as attr(result, "convention").

Examples

parseVariantId(c("chr1:100:A:G", "chr2:200:T:C"))
#> # A tibble: 2 × 4
#>   chrom   pos A2    A1   
#>   <chr> <int> <chr> <chr>
#> 1 1       100 A     G    
#> 2 2       200 T     C