Sample random regions of fixed length.

Sample random regions from the mappable parts of the genome with a given fraction from CpG islands.

Usage

sampleRandomRegions(allowedRegions = NULL, N = 100L, regWidth = 200L)

Arguments

allowedRegions

An unstranded GRanges object of the "allowed" of the genome, usually the mappable regions.

N

Number of regions to sample.

regWidth

Region width.

Value

A GRanges object with randomly sampled mappable regions of width regWidth with fractionCGI coming from CpG islands.

Details

In order to make the results deterministic, set the random number seed before calling sampleRandomRegions using set.seed.

Examples

regs <- GenomicRanges::GRanges(
  seqnames = rep(c("chr1", "chr2"), each = 2), 
  ranges = IRanges::IRanges(start = 1:4, end = 5:8))
set.seed(123)
sampleRandomRegions(regs, N = 2, regWidth = 3L)
#> GRanges object with 2 ranges and 0 metadata columns:
#>       seqnames    ranges strand
#>          <Rle> <IRanges>  <Rle>
#>   [1]     chr1       3-5      *
#>   [2]     chr2       4-6      *
#>   -------
#>   seqinfo: 2 sequences from an unspecified genome; no seqlengths