importVCFfiles: Import VCF Files

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

Usage

importVCFfiles(vcfFiles, sampleNames = NULL)

Arguments

vcfFiles
sampleNames

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 (vcfFiles, sampleNames = NULL) 
{
    my.colnames <- c("CHROM", "POS", "ID", "REF", "ALT", "QUAL", 
        "FILTER", "INFO", "FORMAT", "XTR1", "XTR2", "XTR3")
    if (is.null(sampleNames) | length(sampleNames) != length(vcfFiles)) {
        bypassNames <- paste("sample", 1:length(vcfFiles), sep = ".")
        sampleNames <- vcfFiles
        sampleNames <- sub("\.vcf$", "", sub("^.*(\\|/)", 
            "", tolower(sampleNames)))
        sampleNames[sampleNames == ""] <- bypassNames[sampleNames == 
            ""]
    }
    out <- sapply(1:length(vcfFiles), (function(j) {
        x <- vcfFiles[j]
        if (!is.file(x)) {
            NULL
        }
        else {
            tmpVCF <- read.delim(x, comment.char = "#", header = F, 
                stringsAsFactors = F)
            for (i in 1:ncol(tmpVCF)) {
                colnames(tmpVCF)[i] <- my.colnames[i]
            }
            tmpVCF$SAMPLEID <- sampleNames[j]
            tmpVCF
        }
    }), simplify = FALSE, USE.NAMES = TRUE)
    out <- do.call(rbind, out)
    return(out)
  }

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