Error in running motifBreakR

[amootta]

Hi, I am trying to run motifBreakR with the following command: results <- motifbreakR(snpList = snp_file, pwmList = MotifDb, threshold = 0.90) However, when I try to run it, it gives me this error:

Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 't': subscript out of bounds Calls: motifbreakR ... FUN -> scoreSeqWindows -> t -> .handleSimpleError -> h

I have tried to see if it was a problem wtih my GRanges file but can't seem to find a problem with it so far... however when I was reading in my bed file using: snps.from.file(file = 'prom_flank.bed' , format = "bed",search.genome = BSgenome.Hsapiens.UCSC.hg38) -> snp_file I did receive this warning: Warning message: In snps.from.file(file = "prom_flank.bed", format = "bed", search.genome = BSgenome.Hsapiens.UCSC.hg38) : User selected reference allele differs from the sequence in BSgenome.Hsapiens.UCSC.hg38 continuing with genome specified reference allels there are 131 differences

Could this have lead to the downstream error in running motifBreakR? Please let me know how I can fix this!

Thanks very much

[Simon-Coetzee]

Perhaps your SNP coordinates are off by one? If you have an example of your prom_flank.bed I'll take a look.