Reduce ranges retaining mcols

reduceMC(x, ignore.strand = FALSE, simplify = TRUE, ...)

Arguments

x: A GenomicRanges object
ignore.strand: If set to TRUE, then the strand of x and y is set to "*" prior to any computation.
simplify: logical(1). Attempt to simplify returned columns where possible
...: Passed to reduce

Value

A GRanges object

Details

This function extends reduce so that all mcols are returned in the output. Where the reduced ranges map to multiple ranges in the original range, mcols will be returned as CompressedList columns.

If simplify = TRUE columns will be returned as vectors where possible.

Examples

x <- GRanges(c("chr1:1-10:+", "chr1:6-12:-"))
x$id <- c("range1", "range2")
reduceMC(x)
#> GRanges object with 2 ranges and 1 metadata column:
#>       seqnames    ranges strand |          id
#>          <Rle> <IRanges>  <Rle> | <character>
#>   [1]     chr1      1-10      + |      range1
#>   [2]     chr1      6-12      - |      range2
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
reduceMC(x, ignore.strand = TRUE)
#> GRanges object with 1 range and 1 metadata column:
#>       seqnames    ranges strand |              id
#>          <Rle> <IRanges>  <Rle> | <CharacterList>
#>   [1]     chr1      1-12      * |   range1,range2
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths