genomation (version 1.4.2)

annotateWithFeature: Function to annotate given GRanges object with a given genomic feature

Description

Function to annotate given GRanges object with a given genomic feature

Usage

annotateWithFeature(target, feature, strand = FALSE, extend = 0,
  feature.name = NULL, intersect.chr = FALSE)
## S3 method for class 'GRanges,GRanges':
annotateWithFeature(target, feature,
  strand = FALSE, extend = 0, feature.name = NULL,
  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)

strand

If set to TRUE, annotation features and target features will be overlapped based on strand (def:FAULT)

extend

specifiying a positive value will extend the feature on both sides as much as extend

feature.name

name of the annotation feature. For example: H3K4me1,CpGisland etc. by default the name is taken from the given variable

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(promoters)
annot = annotateWithFeature(cpgi, promoters)