1 | dnmFeat(filename, child.sex, pat.col = 1, mat.col = 2, child.col = 3, genome = "hg18", chrom.conv = "chr")
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filename |
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child.sex |
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pat.col |
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mat.col |
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child.col |
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genome |
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chrom.conv |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 | ##---- 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)
}
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