Get CpG density for genomic regions

Description

Calculate the CpG density for a set of windows

Usage

cpgdensity(subject, chr, pos, windowSize = 500, sequence = "CG")

Arguments

Details

Calculate the CpG density for a set of regions. chr and pos specify the region mid-points and windowSize specifies the size of the window to be centered on these mid-points. i.e. The window will stretch from pos-windowSize/2 to pos+windowSize/2.

Value

a numeric vector

Author(s)

Martin Aryee <aryee@jhu.edu>

Examples

	if (require(BSgenome.Hsapiens.UCSC.hg18)){
		chr <- c("chr1", "chr1", "chr2")
		pos <- c(100000, 100500, 100000)
		cpgd <- cpgdensity(Hsapiens, chr=chr, pos=pos, windowSize = 500)
		cpgd
	}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(charm)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

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    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: SQN
Loading required package: mclust
Package 'mclust' version 5.2
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: nor1mix
Loading required package: fields
Loading required package: spam
Loading required package: grid
Spam version 1.3-0 (2015-10-24) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

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Loading required package: maps

 # maps v3.1: updated 'world': all lakes moved to separate new #
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Attaching package: 'maps'

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Loading required package: RColorBrewer
Loading required package: genefilter
Welcome to charm version 2.18.0
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/charm/cpgdensity.Rd_%03d_medium.png", width=480, height=480)
> ### Name: cpgdensity
> ### Title: Get CpG density for genomic regions
> ### Aliases: cpgdensity
> 
> ### ** Examples
> 
> 	if (require(BSgenome.Hsapiens.UCSC.hg18)){
+ 		chr <- c("chr1", "chr1", "chr2")
+ 		pos <- c(100000, 100500, 100000)
+ 		cpgd <- cpgdensity(Hsapiens, chr=chr, pos=pos, windowSize = 500)
+ 		cpgd
+ 	}
Loading required package: BSgenome.Hsapiens.UCSC.hg18
Loading required package: BSgenome
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'stats4'

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Attaching package: 'S4Vectors'

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Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
[1] 0.000 0.004 0.002
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> dev.off()
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