filterSNV: Filter Single Nucleotide Variants

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

Usage

filterSNV(dataSet, seq_colNames)

Arguments

dataSet
seq_colNames

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 (dataSet, seq_colNames) 
{
    if (!(is.data.frame(dataSet) | is.matrix(dataSet)) | sum(!seq_colNames %in% 
        colnames(dataSet)) > 0 | length(seq_colNames) < 2) {
        stop("Bad input or seq_colNames not found")
    }
    check.tab <- sapply(1:length(seq_colNames), (function(i) {
        tmp <- gsub("[[:space:]]", "", dataSet[, seq_colNames[i]])
        toupper(tmp) %in% c("A", "C", "G", "T")
    }))
    toKeep <- apply(check.tab, 1, (function(rw) {
        sum(rw) == length(rw)
    }))
    out <- dataSet[toKeep, ]
    rownames(out) <- NULL
    return(out)
  }

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