Problems if not all samples have the same chromosomes

[MelinaKlostermann]

Hi,
when I use makeBindingSites, I get the following error
Error in .subset_by_GenomicRanges(x, i) :
‘x’ must have unique names when subsetting by a GenomicRanges subscript.

I think the error comes from the .collapseSamples function, that uses
for (i in seq_along(p)) {
pSum = pSum + p[[i]]
}
This will not add up the chromosomes right if there are different chromosomes or the chromosomes do not have the same order in to samples.

when I merge these two samples

names(signal$signalPlus$1_oe_FLAG)
[1] “KI270802.1” “chr1" “chr10”
[4] “chr11" “chr12” “chr13"
[7] “chr14” “chr15" “chr16”
[10] “chr17" “chr18” “chr19"
[13] “chr2” “chr20" “chr21”
[16] “chr22" “chr3” “chr4"
[19] “chr5” “chr6" “chr7”
[22] “chr8" “chr9” “chrM”
[25] “chrX” “chrY”
names(signal$signalPlus$2_oe_FLAG)
[1] “GL000225.1” “chr1" “chr10”
[4] “chr11" “chr12” “chr13"
[7] “chr14” “chr15" “chr16”
[10] “chr17" “chr18” “chr19"
[13] “chr2” “chr20" “chr21”
[16] “chr22" “chr3” “chr4"
[19] “chr5” “chr6" “chr7”
[22] “chr8" “chr9” “chrM”
[25] “chrX” “chrY”
the merge does not contain “GL000225.1”
names(p)
[1] “KI270802.1" “chr1” “chr10" “chr11” “chr12"
[6] “chr13” “chr14" “chr15” “chr16" “chr17”
[11] “chr18" “chr19” “chr2" “chr20” “chr21"
[16] “chr22” “chr3" “chr4” “chr5" “chr6”
[21] “chr7" “chr8” “chr9" “chrM” “chrX”
[26] “chrY”

instead “KI270802.1” and “GL000225.1" are added and called “KI270802.1”

If I then merge all 4 samples the merge looks like this:
names(sgnMergePlus)
[1] “KI270802.1” “chr1" “chr10”
[4] “chr11" “chr12” “chr13"
[7] “chr14” “chr15" “chr16”
[10] “chr17" “chr18” “chr19"
[13] “chr2” “chr20" “chr21”
[16] “chr22" “chr3” “chr4"
[19] “chr5” “chr6" “chr7”
[22] “chr8" “chr9” “chrM”
[25] “chrX” “chrY” NA
[28] NA

and it will through an error because two names are NA. However, it would probably not cause an error if just one name is NA, which is kind of dangerous. Because it might add up the wrong stuff without causing an error.

[MelinaKlostermann]

I think a fix for the .collapsSamples function would probably be
pSum = p[[1]]
names = unique(unlist(sapply(p, names)))
for (i in 2:length(p)) {
pSum = c(pSum, p[[i]])
pSum = split(pSum, names(pSum))
pSum = lapply(pSum, function(x){
if (length(x)==2){
x = x[[1]] + x[[2]]
}
})
}

[MelinaKlostermann]

Hi, my fault. I updated to BindingSiteFinder Version 1.4.0 and this seems to solve the problem.

bds = BSFDataSetFromBigWig(ranges = pureclip_sites$PURB_oe_FLAG_merged_pureclip_sites_mtp001.bed, meta = meta)
Input ranges are not sorted, sorting for you.
Fixed ranges input, removing chr: GL000009.2 GL000195.1 GL000205.2 GL000213.1 GL000214.1 GL000219.1 GL000220.1 GL000224.1 GL000251.2 GL000252.2 GL000253.2 GL000254.2 GL000255.2 GL000256.2 ...