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!

As the error message suggests, some of your GRanges objects may contain duplicated ranges.

Basically, findOverlapsOfPeaks() calls privateUtil::trimPeakList(), which checks for duplicates and pops out this error if detected.

I think your next step is to double-check your GRanges objects and use unique() to filter out duplicates if any. Below is an example adapted the from usage example of findOverlapsOfPeaks(). Note that peaks3 is identical to peaks2 except that the 4th and 5th ranges are duplicated intentionally for demo.

peaks1 <- GRanges(seqnames=c(6,6,6,6,5),
                 IRanges(start=c(1543200,1557200,1563000,1569800,167889600),
                         end=c(1555199,1560599,1565199,1573799,167893599),
                         names=c("p1","p2","p3","p4","p5")),
                 strand="+")
peaks2 <- GRanges(seqnames=c(6,6,6,6,5),
                  IRanges(start=c(1549800,1554400,1565000,1569400,167888600),
                          end=c(1550599,1560799,1565399,1571199,167888999),
                          names=c("f1","f2","f3","f4","f5")),
                  strand="+")
peaks3 <- GRanges(seqnames=c(6,6,6,6,6),
                  IRanges(start=c(1549800,1554400,1565000,1569400,1569400),
                          end=c(1550599,1560799,1565399,1571199,1571199),
                          names=c("f1","f2","f3","f4","f4")),
                  strand="+")

# Below would pop out error since there are duplicates in peaks3:
t1 <- findOverlapsOfPeaks(peaks1, peaks2, peaks3, maxgap=1000)

Output:
Error in FUN(X[[i]], ...) : Inputs contains duplicated ranges.
             please recheck your inputs.

# To remove duplicates, simply:
peaks4 <- unique(peaks3)
# And below is okay now:
t1 <- findOverlapsOfPeaks(peaks1, peaks2, peaks4, maxgap=1000)

# To find out which rows are duplicated, the following codes may help:
df <- data.frame(peaks3)
df[duplicated(df), ]

Output:
  seqnames   start     end width strand
5        6 1569400 1571199  1800      +