R/AllGenerics.R, R/partitionRanges.R
partitionRanges-methods.RdPartition a set of Genomic Ranges by another
partitionRanges(x, y, ...)
# S4 method for class 'GRanges,GRanges'
partitionRanges(
x,
y,
y_as_both = TRUE,
ignore.strand = FALSE,
simplify = TRUE,
suffix = c(".x", ".y"),
...
)GenomicRanges objects
Not used
logical(1) If there are any unstranded regions in y, should these be assigned to both strands. If TRUE unstranded regions can be used to partition stranded regions
If set to TRUE, then the strand of x and y is set to "*" prior to any computation.
Pass to chopMC and simplify mcols in the output
Added to any shared column names in the provided objects
A GRanges object
The query set of ranges can be broken in regions which strictly overlap a second set of ranges. The complete set of mcols from both initial objects will included in the set of partitioned ranges
x <- GRanges(c("chr1:1-10", "chr1:6-15"))
x$id <- paste0("range", seq_along(x))
x
#> GRanges object with 2 ranges and 1 metadata column:
#> seqnames ranges strand | id
#> <Rle> <IRanges> <Rle> | <character>
#> [1] chr1 1-10 * | range1
#> [2] chr1 6-15 * | range2
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
y <- GRanges(c("chr1:2-5", "chr1:6-12"))
y$id <- paste0("range", seq_along(y))
y
#> GRanges object with 2 ranges and 1 metadata column:
#> seqnames ranges strand | id
#> <Rle> <IRanges> <Rle> | <character>
#> [1] chr1 2-5 * | range1
#> [2] chr1 6-12 * | range2
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
partitionRanges(x, y)
#> GRanges object with 5 ranges and 2 metadata columns:
#> seqnames ranges strand | id.y id.x
#> <Rle> <IRanges> <Rle> | <character> <character>
#> [1] chr1 1 * | <NA> range1
#> [2] chr1 2-5 * | range1 range1
#> [3] chr1 6-10 * | range2 range1
#> [4] chr1 6-12 * | range2 range2
#> [5] chr1 13-15 * | <NA> range2
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths