Nothing
set.genomic.region.subregion <- function(x, regions, subregions, split = TRUE) {
if(!is.factor(regions$Name) | !is.factor(subregions$Name)) stop("regions$Name and subregions$Name should be factors with levels ordered in the genome order")
# ce test est OK pour les facteurs aussi
if(typeof(x@snps$chr) != "integer")
stop("x@snps$chr should be either a vector of integers, or a factor with same levels as regions$Chr")
#Add one to start to take into account bed format
regions$Start <- regions$Start + 1
# remove duplicated regions if any
w <- duplicated(regions$Name)
if(any(w)) {
regions <- regions[!w,]
}
# check if regions is sorted by chr / starting pos
n <- nrow(regions)
chr1 <- regions$Chr[1:(n-1)]
chr2 <- regions$Chr[2:n]
b <- (chr1 < chr2) | (chr1 == chr2 & regions$Start[1:(n-1)] <= regions$Start[2:n])
if(!all(b)) {
regions <- regions[ order(regions$Chr, regions$Start), ]
}
# check if subregions is sorted by chr / starting pos
n <- nrow(subregions)
chr1 <- subregions$Chr[1:(n-1)]
chr2 <- subregions$Chr[2:n]
b <- (chr1 < chr2) | (chr1 == chr2 & subregions$Start[1:(n-1)] <= subregions$Start[2:n])
if(!all(b)) {
subregions <- subregions[ order(subregions$Chr, subregions$Start), ]
}
###Annotation region
R <- .Call("label_multiple_genes", PACKAGE = "Ravages", regions$Chr, regions$Start, regions$End, x@snps$chr, x@snps$pos)
R.genename <- unlist(lapply(R, function(z) paste(levels(regions$Name)[unlist(z)], collapse=",")))
R.genename[which(R.genename=="")] <- NA
x@snps$genomic.region <- R.genename
x@snps$genomic.region <- factor(x@snps$genomic.region, levels = unique(x@snps$genomic.region))
if(any(grepl(x@snps$genomic.region, pattern = ","))){
x <- bed.matrix.split.genomic.region(x, genomic.region = x@snps$genomic.region, split.pattern = ",")
}
###Annotation subregion
Rsub <- .Call("label_multiple_genes", PACKAGE = "Ravages", subregions$Chr, subregions$Start, subregions$End, x@snps$chr, x@snps$pos)
Rsub.genename <- unlist(lapply(Rsub, function(z) paste(subregions$Name[unlist(z)], collapse=",")))
Rsub.genename[which(Rsub.genename=="")] <- NA
x@snps$SubRegion <- Rsub.genename
x@snps$SubRegion <- factor(x@snps$SubRegion, levels = unique(x@snps$SubRegion))
#if(any(grepl(x@snps$SubRegion, pattern = ","))){
# x <- bed.matrix.split.genomic.region(x, genomic.region = x@snps$SubRegion, split.pattern = ",")
#}
x
}
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