R/al2bp.R

In seqinr: Biological Sequences Retrieval and Analysis

al2bp <- function(allele.name, repeat.bp = 4, offLadderChars = "><", split = "\\."){
    allele.name <- as.character(allele.name)
    if(any(s2c(allele.name) %in% s2c(offLadderChars))) return(NA)	
    dec <- unlist(strsplit(allele.name, split = split))
    res <- repeat.bp*suppressWarnings(as.numeric(dec[1]))
    # NA are returned for X and Y at Amelogenin locus for instance
    if(length(dec) > 1) res <- res + as.numeric(dec[2])
    return(res)
}