Calculates the distance to the next range in the target and query genome.
Usage
dist2next(x, step = 1, ignore.strand = FALSE)
# S4 method for class 'GRanges'
dist2next(x, step = 1, ignore.strand = FALSE)
# S4 method for class 'GBreaks'
dist2next(x, step = 1, ignore.strand = FALSE)Arguments
- x
A
GRangesor aGBreaksobject.- step
Distance to the nth block (default: first).
- ignore.strand
Calculate distance for ranges on different strands.
Value
For GRanges, returns the object with one extra metadata colums,
dist, and for GBreaks two extra columns tdist and qdist, containing
the distance to the next range in the reference and query genomes
respectively.
Details
The distance is defined by the GenomicRanges::distance function. Note
that because the last range has not next neighbor, the last value is set
to Inf arbitrarily.
See also
Other Colinearity functions:
GOC(),
bridgeRegions(),
chain_contigs(),
coalesce_contigs(),
filterColinearRegions(),
flagColinearAlignments(),
flagPairs()
Examples
dist2next(exampleInversion)
#> GBreaks object with 3 ranges and 3 metadata columns:
#> seqnames ranges strand | query tdist qdist
#> <Rle> <IRanges> <Rle> | <GRanges> <numeric> <numeric>
#> [1] chrA 100-190 + | chrB:100-190 NA 20
#> [2] chrA 210-291 - | chrB:210-291 NA 10
#> [3] chrA 301-400 + | chrB:301-400 Inf Inf
#> -------
#> seqinfo: 1 sequence from an unspecified genome
dist2next(granges(exampleInversion))
#> GRanges object with 3 ranges and 1 metadata column:
#> seqnames ranges strand | dist
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] chrA 100-190 + | NA
#> [2] chrA 210-291 - | NA
#> [3] chrA 301-400 + | Inf
#> -------
#> seqinfo: 1 sequence from an unspecified genome
dist2next(exampleInversion, ignore.strand = TRUE)
#> GBreaks object with 3 ranges and 3 metadata columns:
#> seqnames ranges strand | query tdist qdist
#> <Rle> <IRanges> <Rle> | <GRanges> <numeric> <numeric>
#> [1] chrA 100-190 + | chrB:100-190 20 20
#> [2] chrA 210-291 - | chrB:210-291 10 10
#> [3] chrA 301-400 + | chrB:301-400 Inf Inf
#> -------
#> seqinfo: 1 sequence from an unspecified genome
dist2next(exampleInversion - 20, ignore.strand = TRUE)
#> GBreaks object with 3 ranges and 3 metadata columns:
#> seqnames ranges strand | query tdist qdist
#> <Rle> <IRanges> <Rle> | <GRanges> <numeric> <numeric>
#> [1] chrA 120-170 + | chrB:100-190 60 20
#> [2] chrA 230-271 - | chrB:210-291 50 10
#> [3] chrA 321-380 + | chrB:301-400 Inf Inf
#> -------
#> seqinfo: 1 sequence from an unspecified genome
dist2next(exampleInversion, 2)
#> GBreaks object with 3 ranges and 3 metadata columns:
#> seqnames ranges strand | query tdist qdist
#> <Rle> <IRanges> <Rle> | <GRanges> <numeric> <numeric>
#> [1] chrA 100-190 + | chrB:100-190 111 111
#> [2] chrA 210-291 - | chrB:210-291 Inf Inf
#> [3] chrA 301-400 + | chrB:301-400 Inf Inf
#> -------
#> seqinfo: 1 sequence from an unspecified genome