methylPipe (version 1.6.2)

getCpos: Get genomic Cxx positons for a series of genomic regions

Description

getCpos retrieves genomic Cxx positions, possible target of DNA methylation for a series of genomic regions (and bins thereof) and a given organism. getCposChr is a Helper function which performs the same task for any given DNAString sequence and is not intended for the user to call directly.

Usage

getCpos(GenoRanges, seqContext='all', nbins, org)
getCposChr(GenoRanges, seqContext, chrseq, nbins)

Arguments

GenoRanges

An object of class GRanges

seqContext

character; one of: all, CG, CHG or CHH

org

an object of class BSgenome; typically the genome sequences of a given organism

chrseq

an object of class DNAString; typically a chromosome sequence of a given organism

nbins

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

Value

• A list is returned with the position of the Cxx in the GRanges regions. The length of the list is equal to the length of the GRanges. For each list item a list with length equal to the number of bins of the GRanges is returned. For each bin the position of the Cxx relative to the genomic coordinates of that bin is returned.

See Also

getCposDensity, profileDNAmetBin

Examples

require(BSgenome.Hsapiens.UCSC.hg18)
gr_file <- system.file('extdata', 'GR_chr20.Rdata', package='methylPipe')
load(gr_file)
res <- getCpos(GR_chr20, seqContext='CG', nbins=1, org=Hsapiens)
res[[1]]