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

Description Usage Arguments Value Examples

Description

Function to annotate given GRanges object with a given genomic feature

Usage

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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

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BIMSBbioinfo/genomation documentation built on Feb. 4, 2018, 12:11 p.m.