annotateWithFeature-methods: Function to annotate given GRanges object with a given...

In genomation: Summary, annotation and visualization of genomic data

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)

## S4 method for signature '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)

genomation documentation built on Nov. 8, 2020, 5:21 p.m.