Hello! I keep getting the following error from running findOverlapsOfPeaks using ChIPpeakAnno and I would love advice!
I ran this same code on a different broadpeak file set I made from a dataframe and it worked fine, however, with this dataset it does not. I'm really not changing anything except the contents of the dataframe, but they each have the same columns and were built the same way.
#make a new df keeping only the columns for broadpeak BED format. annoIDsNdf_upTSS8kb %>% select(seqnames, start, end, peak, score, strand, signalValue, pValue, qValue) -> upTSS8kb_N.broadpeak upTSS8kb_N.broadpeak %>% rename( chrom = seqnames, chromStart = start, chromEnd = end, name = peak, ) ##done for all 4 samples #makes gRanges from above files upTSS8kb_Ngr <- toGRanges(upTSS8kb_N.broadpeak, format="broadPeak") upTSS8kb_Hgr <- toGRanges(upTSS8kb_H.broadpeak, format="broadPeak") upTSS8kb_8gr <- toGRanges(upTSS8kb_8.broadpeak, format="broadPeak") upTSS8kb_5gr <- toGRanges(upTSS8kb_5.broadpeak, format="broadPeak") #find overlapping peaks ol_NHP_upTSS8kb <- findOverlapsOfPeaks(upTSS8kb_Ngr, upTSS8kb_Hgr, upTSS8kb_8gr, upTSS8kb_5gr)
output of the last line is:
Error in FUN(X[[i]], ...) : Inputs contains duplicated ranges. please recheck your inputs.
I appreciate any and all help. Thank you!