R/misc.R

In Bioconductor/Biostrings: Efficient manipulation of biological strings

### Some miscellaneous stuff

N50 <- function(csizes)
{
    if (!is.numeric(csizes))
        stop("'csizes' must be a vector containing the contig sizes")
    #If only integer, then genome size maxes out at 2.1Gbp, so coerce to double:
    if(is.integer(csizes))
        csizes <- as.numeric(csizes)
    decreasing_csizes <- sort(csizes, decreasing=TRUE)
    tmp <- cumsum(decreasing_csizes)
    total_size <- tmp[length(tmp)]
    N50 <- decreasing_csizes[which(tmp >= total_size/2)[1]]
    return(N50)
}