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

Description Usage Arguments Value Author(s) See Also Examples

View source: R/Allfunctions.R

Description

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

Usage

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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.

Author(s)

Mattia Pelizzola

See Also

getCpos, profileDNAmetBin

Examples

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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)

methylPipe documentation built on Nov. 8, 2020, 6:51 p.m.