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

In fortunatobianconi/methylkit: DNA methylation analysis from high-throughput bisulfite sequencing results

Description

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

Usage

  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

# 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"))

fortunatobianconi/methylkit documentation built on May 16, 2019, 1:51 p.m.