removeMismatchMut: Remove Mutations Corresponding to Mismatched Reference...

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

Usage

removeMismatchMut(mutData, refMut_colName = "mutation", context_colName = "context", refMut_format = "N>N")

Arguments

mutData
refMut_colName
context_colName
refMut_format

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 (mutData, refMut_colName = "mutation", context_colName = "context", 
    refMut_format = "N>N") 
{
    if (!((is.data.frame(mutData) | is.matrix(mutData)) & sum(c(refMut_colName, 
        context_colName) %in% colnames(mutData)) == 2)) 
        stop("Issue with the input dataset. Make sure to feed in a data.frame or\n          a matrix and double check the name of the fields pointing to chromosome\n          name, start and end positions")
    if (!refMut_format %in% c("N>N", "N")) 
        stop("Unrecognized refMut_format")
    output <- data.frame(mutData, stringsAsFactors = FALSE, row.names = NULL)
    colnames(output) <- colnames(mutData)
    if (refMut_format == "N>N") {
        output$mutSite.dnaSeq.Ref <- substr(mutData[, refMut_colName], 
            1, 1)
        output$mutSite.dnaSeq.Mut <- substr(mutData[, refMut_colName], 
            3, 3)
        refMut_colName <- "mutSite.dnaSeq.Ref"
    }
    pos.to.extr <- (0.5 * (nchar(output[, context_colName]) - 
        1)) + 1
    keep.id <- output[, refMut_colName] == substr(output[, context_colName], 
        pos.to.extr, pos.to.extr)
    if (sum(keep.id == FALSE) > 0) 
        message(paste("Removing", sum(keep.id == FALSE), "rows because of mismatch"))
    output <- output[keep.id, ]
    rownames(output) <- NULL
    return(output)
  }

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