Error in .subset_by_GenomicRanges(x, i): 'x' must have unique names when subsetting by a GenomicRanges subscript about bindingsitefinder HOT 4 CLOSED

Hi @muzyuri ,

sorry for the late reply. Did you fixed it in the meantime?

If not what does the output of the makeBindingSites() function looks like? Does it produce the same error?

It seems like there is an issue with the names in of your GRanges object and/ or the seqnames (names for the chromosomes). Can you once make sure that the seqnames in the GRanges object match with the names of the signal object. You can do this by doing sth by looking into head(names(getSignal(bds)[[1]][[1]])) and head(seqnames(getRanges(bds))).

Besides that, maybe the '_' in the seqnames is causing the trouble.

I hope this is still helpful for you, even tough the reply was so late.

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Hi @MirkoBr, thank you for your kindly support!

I am still stacking here.
After your reply, I checked my GRanges object and the seqnames and made sure that the seqnames in the GRanges object matched with the names of the signal object.
Besides, I removed all '_' and '-' in the seqnames and retried to proceed with the workflow like this:

supportRatioPlot(bds, bsWidths = seq(from = 3, to = 19, by = 2))

but I got the following another error:

Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'flesh' in selecting a method for function 'relist': subscript contains out-of-bounds ranges

I also got this same error in the makeBindingSites() function.

Do you have any idea what is wrong? Thanks a lot in advance.

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Hi @muzyuri,

the error message that you get is a very general one. So without seeing some of your objects it's hard to tell where it goes wrong.

Could you provide a small subset of your data. Just like the first 10-20 entries in the GRanges plus the iCLIP signal for these ranges? To get both sets, see the code snippet below.

library(BindingSiteFinder)

# subset the GRanges object
rangesSubset = head(getRanges(bds), 20)

# subset the RLE signal list
totalSignal = signal$signalPlus$`1_WT`$chr22
startAt = max(as.data.frame(ranges(totalSignal))$start)
endAt = min(as.data.frame(ranges(totalSignal))$start)
signalSubset = totalSignal[startAt:endAt]

# save both objects
saveRDS(rangesSubset, file = "./rangesSubset.rds")
saveRDS(signalSubset, file = "./signalSubset.rds")

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fixed in 10ce962

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