getCposDensity: Determines the density of genomic Cxx positions for a series...
In kamalfartiyal84/methylPipe: Base resolution DNA methylation data analysis

Description Usage Arguments Value Author(s) See Also Examples

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

1	getCposDensity(GenoRanges, Cpos, nbins)

`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

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

Mattia Pelizzola

getCpos, profileDNAmetBin

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)