read.feature.flank-methods: a function to read-in genomic features and their upstream and...

Description Usage Arguments Value Examples

Description

a function to read-in genomic features and their upstream and downstream adjecent regions such as CpG islands and their shores

Usage

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  read.feature.flank(location,remove.unsual=TRUE,flank=2000,clean=TRUE,feature.flank.name=NULL)

Arguments

location

for the bed file of the feature

flank

number of basepairs for the flanking regions

clean

If set to TRUE, flanks overlapping with other main features will be trimmed

remove.unsual

remove chromsomes with unsual names random, Un and antyhing with "_" character

feature.flank.name

the names for feature and flank ranges, it should be a character vector of length 2. example: c("CpGi","shores")

Value

a GenomicRangesList contatining one GRanges object for flanks and one for GRanges object for the main feature.

Examples

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# location of the example CpG file
 my.loc=system.file("extdata", "cpgi.hg18.bed.txt", package = "methylKit")
 cpg.obj=read.feature.flank(location=my.loc,feature.flank.name=c("CpGi","shores"))

tectronics/methylkit documentation built on May 27, 2017, 4:14 a.m.