annotateWithFeatureFlank {genomation} | R Documentation

## Function to annotate a given GRanges object with promoter,exon,intron & intergenic values

### Description

Function to annotate a given GRanges object with promoter,exon,intron & intergenic values

### Usage

    annotateWithFeatureFlank(target, feature, flank, feature.name = NULL,
      flank.name = "flank", strand = FALSE, intersect.chr = FALSE)

    ## S4 method for signature 'GRanges,GRanges,GRanges'
    annotateWithFeatureFlank(target, feature,
      flank, feature.name = NULL, flank.name = "flank", strand = FALSE,
      intersect.chr = FALSE)

### Arguments

`target` | a granges object storing chromosome locations to be annotated
`feature` | a granges object storing chromosome locations of a feature (can be CpG islands, ChIP-seq peaks, etc)
`flank` | a granges object storing chromosome locations of the flanks of the feature
`feature.name` | string for the name of the feature
`flank.name` | string for the name of the flanks
`strand` | If set to TRUE, annotation features and target features will be overlapped based on strand (def:FAULT)
`intersect.chr` | boolean, whether to select only chromosomes that are common to feature and target. FALSE by default

### Value

returns an `AnnotationByFeature` object

### Examples

    data(cpgi)
    data(cage)
    cpgi.flanks = getFlanks(cpgi)
    flank.annot = annotateWithFeatureFlank(cage, cpgi, cpgi.flanks)

[Package genomation version 1.11.3 Index]