methylPipe (version 1.6.2)

getCposDensity: Determines the density of genomic Cxx positions for a series of genomic regions

Description

After having used getCpos (or getCposChr), getCposDensity determines the density of Cxx sites for each bin of each genomic region.

Usage

getCposDensity(GenoRanges, Cpos, nbins)

Arguments

GenoRanges

an object of class GRanges used to generate the Cpos list

Cpos

list returned by getCpos or getCposChr methods

nbins

numeric; the number of bins each region of genomic regions is divided

Value

• Returns a list with the number of Cxx sites per bp of bin size for each region of the GRanges.

See Also

getCpos, profileDNAmetBin

Examples

require(BSgenome.Hsapiens.UCSC.hg18)
gr_file <- system.file('extdata', 'GR_chr20.Rdata', package='methylPipe')
load(gr_file)
resC <- getCposChr(GenoRanges=GR_chr20, seqContext='CG', chrseq=unmasked(Hsapiens[['chr20']]), nbins=3)
resd <- getCposDensity(GenoRanges=GR_chr20, Cpos= resC, nbins=3)