genomation (version 1.4.2)

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

Description

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

Usage

readFeatureFlank(location,remove.unusual=TRUE,flank=2000,
                        clean=TRUE,feature.flank.name=NULL)
## S3 method for class 'character':
readFeatureFlank(location, remove.unusual = TRUE,
  flank = 2000, clean = TRUE, feature.flank.name = NULL)

Arguments

location

for the bed file of the feature.

remove.unusual

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

flank

number of basepairs for the flanking regions

clean

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

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. NOTE: This can not return a GRangesList at the moment because flanking regions do not have to have the same column name as the feature. GRangesList elements should resemble each other in the column content. We can not satisfy that criteria for the flanks

Examples

cgi.path = system.file('extdata/chr21.CpGi.hg19.bed', package='genomation')
cgi.shores = readFeatureFlank(cgi.path)
cgi.shores