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

In BIMSBbioinfo/genomation: Summary, annotation and visualization of genomic data

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)

BIMSBbioinfo/genomation documentation built on March 13, 2020, 5:28 a.m.