readFeatureFlank {genomation} | R Documentation

## 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)

    ## S4 method for signature '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

[Package genomation version 1.22.0 Index]