genomation (version 1.4.2)

annotateWithFeatureFlank: 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)
## S3 method for class '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)