revCompl: Reverse Complement of a Nucleic Acid Sequence

In dami82/mutSignatures_dev: Decipher Mutational Signatures from Somatic Mutational Catalogs

Usage

revCompl(DNAseq, rev = TRUE, compl = TRUE)

Arguments

DNAseq
rev
compl

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (DNAseq, rev = TRUE, compl = TRUE) 
{
    if (is.character(DNAseq)) {
        resultVect <- sapply(DNAseq, (function(seqString) {
            mySeq <- toupper(seqString)
            if (rev == TRUE) {
                mySeq <- paste(sapply(1:nchar(mySeq), (function(i) {
                  pos <- nchar(mySeq) + 1 - i
                  substr(mySeq, pos, pos)
                })), collapse = "")
            }
            if (compl == TRUE) {
                mySeq <- paste(sapply(1:nchar(mySeq), (function(i) {
                  aBase <- substr(mySeq, i, i)
                  complBase <- c("A", "T", "C", "G", "N", "A")
                  names(complBase) <- c("T", "A", "G", "C", "N", 
                    "U")
                  returnBase <- complBase[aBase]
                  if (is.na(returnBase)) {
                    stop("Bad input")
                  }
                  returnBase
                })), collapse = "")
            }
            return(mySeq)
        }))
        names(resultVect) <- NULL
        return(resultVect)
    }
    else {
        warning("Bad input")
    }
  }

dami82/mutSignatures_dev documentation built on May 17, 2019, 7:02 p.m.