genomeBlocks: Creates bins across a genome.

In Repitools: Epigenomic tools

Description

Creates a compact GRanges representation of bins across specified chromosomes of a given genome.

Usage

  ## S4 method for signature 'numeric'
genomeBlocks(genome, chrs = names(genome), width = NULL,
                                   spacing = width)
  ## S4 method for signature 'BSgenome'
genomeBlocks(genome, chrs = seqnames(genome), width = NULL,
                                    spacing = width)

Arguments

genome	Either a BSgenome object, or a named vector of integers (names being choromosome names, integers being the chromosome lengths), to get the chromosome lengths from.
chrs	A vector containing which chromosomes to create bins across. May either be numeric indicies or chromosome names. Default is all chromosomes given by genome.
width	The width in base pairs of each bin.
spacing	The space between the centres of each adjacent bin. By default, is equal to the spacing parameter, which gives non-overlapping bins. Values larger than spacing will give overlapping bins, and values smaller than spacing will give gaps between each bin.

Value

Returns a GRanges object, compatible with direct usage in annotationBlocksCounts

Author(s)

Aaron Statham

See Also

annotationBlocksCounts

Examples

  chr.lengths <- c(800, 200, 200)
  names(chr.lengths) <- c("chr1", "chr2", "chr3")
  genomeBlocks(chr.lengths, width = 200)

Repitools documentation built on Nov. 8, 2020, 7:52 p.m.