getCpos: Get genomic Cxx positons for a series of genomic regions
In methylPipe: Base resolution DNA methylation data analysis

Description Usage Arguments Value Author(s) See Also Examples

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.

1 2	getCpos(GenoRanges, seqContext='all', nbins, org) getCposChr(GenoRanges, seqContext, chrseq, nbins)

`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

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.

Mattia Pelizzola

getCposDensity, profileDNAmetBin

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]]