R/revcomp.R

In GuangchuangYu/skleid: State Key Lab of Emerging Infectious Diseases

##' reverse complement of DNA string
##'
##' 
##' @title revcomp
##' @param seq DNA sequence string
##' @return character
##' @author ygc
##' @export
revcomp <- function(seq) {
    ## complement
    seq <- toupper(seq)
    seq2 <- chartr("ATCGMKRYWSVBHDXN", "TAGCKMYRWSBVDHXN", seq)
    ## vectorize
    seq2 <- substring(seq2, 1:nchar(seq2), 1:nchar(seq2))
    ## reverse
    x <- paste(rev(seq2), collapse="")
    return(x)	
}