getCposDensity {methylPipe} | R Documentation

## 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.

### Author(s)

Mattia Pelizzola

### 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)

[Package methylPipe version 1.16.0 Index]