patchwork.alleledata <- function (Pileup, vcf, hg_build)
{
packagepath = system.file(package = "patchwork")
system(paste("cp -r ", packagepath, "/python .python", sep = ""))
system(paste("python .python/mpile2alleles.py ", vcf, " >",
getwd(), "/pile.alleles", sep = ""))
system("rm -r .python")
alf = read.csv("pile.alleles", sep = "\t", header = F)[,
1:6]
colnames(alf) = c("achr", "apos", "atype", "aqual", "atot",
"amut")
alf$aref = alf$atot - alf$amut
alf$amax = apply(alf[, 6:7], 1, max)
alf$amin = alf$atot - alf$amax
if (length(grep("M", alf$achr)) != 0) {
alf = alf[-grep("M", alf$achr), ]
}
alf$achr = as.character(alf$achr)
x_x = strsplit(alf$achr[1], "chr")
if (length(x_x[[1]]) == 1) {
for (i in 1:22) {
alf$achr[alf$achr == as.character(i)] = paste("chr",
as.character(i), sep = "")
}
i = "X"
alf$achr[alf$achr == as.character(i)] = paste("chr",
as.character(i), sep = "")
i = "Y"
alf$achr[alf$achr == as.character(i)] = paste("chr",
as.character(i), sep = "")
}
if (hg_build == "hg18") {
data(commonSnpsHG18, package = "patchworkData")
}
else if (hg_build == "hg19") {
data(commonSnps132, package = "patchworkData")
}
dbSnp = dbSnp[, c(1, 3)]
dbSnp$dbSnp = T
alf = merge(alf, dbSnp, all.x = T, all.y = F, by = 1:2)
alf$dbSnp[is.na(alf$dbSnp)] = F
return(alf)
}
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