dnmFeat: A wrapper to create features from all chromosomes in a...

In mbelmadani/forestDNM-archive: Predicts de novo SNVs when provided a VCF containing variants of a genotyped family.

Usage

dnmFeat(filename, child.sex, pat.col = 1, mat.col = 2, child.col = 3, genome = "hg18", chrom.conv = "chr")

Arguments

filename
child.sex
pat.col
mat.col
child.col
genome
chrom.conv

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 (filename, child.sex, pat.col = 1, mat.col = 2, child.col = 3, 
    genome = "hg18", chrom.conv = "chr") 
{
    require(VariantAnnotation)
    if (missing(child.sex) || !child.sex %in% c("M", "F")) 
        stop("offspring's sex must be specified (M or F)")
    chr = paste(chrom.conv, c(1:22), sep = "")
    X = list()
    for (i in 1:length(chr)) {
        rg = RangedData(IRanges(start = 1, end = 3e+08), space = chr[i])
        param <- ScanVcfParam(which = rg, geno = c("AD", "DP", 
            "GQ", "GT", "PL"), info = c("VQSLOD", "SB", "DB", 
            "BaseQRankSum", "Dels", "FS", "HaplotypeScore", "MQ", 
            "MQRankSum", "QD", "ReadPosRankSum", "AN"))
        vcf = readVcf(filename, genome, param)
        X[[i]] = pDNM(vcf, pat.col, mat.col, child.col)
        print(paste("done with", chr[i]))
    }
    if (child.sex == "M") {
        rg = RangedData(IRanges(start = 1, end = 3e+08), space = paste(chrom.conv, 
            "X", sep = ""))
        param <- ScanVcfParam(which = rg, geno = c("AD", "DP", 
            "GQ", "GT", "PL"), info = c("VQSLOD", "SB", "DB", 
            "BaseQRankSum", "Dels", "FS", "HaplotypeScore", "MQ", 
            "MQRankSum", "QD", "ReadPosRankSum", "AN"))
        vcf = readVcf(filename, genome, param)
        X[[23]] = pDNM_X_male(vcf, pat.col, mat.col, child.col)
        print("done with chrX")
        rg = RangedData(IRanges(start = 1, end = 3e+08), space = paste(chrom.conv, 
            "Y", sep = ""))
        param <- ScanVcfParam(which = rg, geno = c("AD", "DP", 
            "GQ", "GT", "PL"), info = c("VQSLOD", "SB", "DB", 
            "BaseQRankSum", "Dels", "FS", "HaplotypeScore", "MQ", 
            "MQRankSum", "QD", "ReadPosRankSum", "AN"))
        vcf = readVcf(filename, genome, param)
        X[[24]] = pDNM_Y(vcf, pat.col, child.col)
        X = do.call("rbind", X)
        print("done with chrY")
    }
    else {
        rg = RangedData(IRanges(start = 1, end = 3e+08), space = paste(chrom.conv, 
            "X", sep = ""))
        param <- ScanVcfParam(which = rg, geno = c("AD", "DP", 
            "GQ", "GT", "PL"), info = c("VQSLOD", "SB", "DB", 
            "BaseQRankSum", "Dels", "FS", "HaplotypeScore", "MQ", 
            "MQRankSum", "QD", "ReadPosRankSum", "AN"))
        vcf = readVcf(filename, genome, param)
        X[[23]] = pDNM_X_female(vcf, pat.col, mat.col, child.col)
        X = do.call("rbind", X)
        print("done with chrX")
    }
    X = X[!duplicated(paste(X$chr, X$pos, sep = ":")), ]
    return(X)
  }

mbelmadani/forestDNM-archive documentation built on May 30, 2019, 2:17 p.m.