Rtracklayer exporting Granges object as bigwig error: Features cannot overlap
1
0
Entering edit mode
ssabri ▴ 20
@ssabri-9464
Last seen 4.6 years ago

I have a granges object that I'm trying to export as a BigWig. The object looks like this:

> prediction
GRanges object with 4127167 ranges and 1 metadata column:
            seqnames              ranges strand |             score
               <Rle>           <IRanges>  <Rle> |         <numeric>
        [1]     chr1           5201-5400      * | 0.704062535636186
        [2]     chr1           5401-5600      * |   0.7038285233713
        [3]     chr1           5601-5800      * | 0.703379269216662
        [4]     chr1           5801-6000      * | 0.703339211770708
        [5]     chr1           6001-6200      * | 0.703186993302055
        ...      ...                 ...    ... .               ...
  [4127163]     chrX 155190601-155190800      * |   0.3657433841594
  [4127164]     chrX 155190801-155191000      * | 0.365798827160496
  [4127165]     chrX 155191001-155191200      * | 0.366063557897697
  [4127166]     chrX 155191201-155191400      * | 0.366739565616863
  [4127167]     chrX 155191401-155191600      * | 0.367196219763251
  -------
  seqinfo: 23 sequences from hg19 genome

> seqinfo(prediction)
Seqinfo object with 23 sequences from hg19 genome:
  seqnames seqlengths isCircular genome
  chr1      249250621       <NA>   hg19
  chr2      243199373       <NA>   hg19
  chr3      198022430       <NA>   hg19
  chr4      191154276       <NA>   hg19
  chr5      180915260       <NA>   hg19
  ...             ...        ...    ...
  chr19      59128983       <NA>   hg19
  chr20      63025520       <NA>   hg19
  chr21      48129895       <NA>   hg19
  chr22      51304566       <NA>   hg19
  chrX      155270560       <NA>   hg19

I have been using the export.bw feature from the rtracklayer R package in other cases successfully but for this case I run into an error that states:

>  rtracklayer::export.bw(prediction, con = "file.bw")
Error in FUN(extractROWS(unlisted_X, IRanges(X_elt_start[i], X_elt_end[i])),  : 
  Features cannot overlap. Note that WIG does not distinguish between strands - try exporting two tracks, one for each strand.

From what I see there aren't overlapping regions? All widths of the ranges are set at 200bps. Is there a way to check and remove/fix overlapping ranges?

EDIT: I've also tried to export by each chromosome split out and was returned a similar error:

prediction_by_chr <- split(prediction, f = seqnames(prediction))
lapply(seq_along(prediction_by_chr), function(x){
  chr <- names(prediction_by_chr)[x]; message(chr)
  rtracklayer::export.bw(prediction_by_chr[[chr]], con = "file.bw")  
})

Error in FUN(extractROWS(unlisted_X, IRanges(X_elt_start[i], X_elt_end[i])),  : 
  BigWig ranges cannot overlap

EDIT2: This solution seems to fix the issue by removing those overlaps:

hits <- findOverlaps(prediction, prediction)
overlaps <- hits[hits@from != hits@to]
o <- data.frame(seqnames = unlist(extractList(seqnames(prediction), overlaps)), 
                start = unlist(extractList(start(prediction), overlaps)), 
                end = unlist(extractList(end(prediction), overlaps)))
o_gr <- GenomicRanges::makeGRangesFromDataFrame(o)
prediction_fixed <- prediction[!(prediction %over% o_gr)]
rtracklayer genomicranges granges • 2.7k views
ADD COMMENT
1
Entering edit mode
@michael-lawrence-3846
Last seen 2.9 years ago
United States

You can drop the overlapping ranges with something like:

hits <- findOverlaps(prediction, drop.self=TRUE)
prediction_fixed <- prediction[-queryHits(hits)]
ADD COMMENT

Login before adding your answer.

Traffic: 634 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6