Open gevro opened 2 years ago
Hi, For some reason the below setdiff is not filtering out the element in x, even though it is encompassed by y.
x:
> mutations.gr[[1]][2] GRanges object with 1 range and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> [1] chr1 15003249 + ------- seqinfo: 23 sequences from an unspecified genome; no seqlengths
y:
> genes[266] GRanges object with 1 range and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> [1] chr1 14971680-15048506 * ------- seqinfo: 24 sequences from an unspecified genome; no seqlengths
> setdiff(mutations.gr[[1]][2],genes[266]) GRanges object with 1 range and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> [1] chr1 15003249 + ------- seqinfo: 24 sequences from an unspecified genome; no seqlengths
=> The result should be an empty GRanges.
But adding ignore.strand=TRUE works:
> setdiff(mutations.gr[[1]][2],genes[266],ignore.strand=TRUE) GRanges object with 0 ranges and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> ------- seqinfo: 24 sequences from an unspecified genome; no seqlengths
Shouldn't setdiff of a range with strand = + that is encompassed by a range with strand = * be considered an overlap and removed by setdiff?
Hi, For some reason the below setdiff is not filtering out the element in x, even though it is encompassed by y.
x:
y:
=> The result should be an empty GRanges.
But adding ignore.strand=TRUE works:
Shouldn't setdiff of a range with strand = + that is encompassed by a range with strand = * be considered an overlap and removed by setdiff?