annotateAnchors: Add meta data column to anchors based on GRanges

In aryeelab/diffloop: Identifying differential DNA loops from chromatin topology data

Description

annotateAnchors adds a logical variable to meta data columns in the anchors based on a GRanges object of features' genomic coordinates

Usage

annotateAnchors(dlo, features, featureName, maxgap)

## S4 method for signature 'loops,GRanges,character,missing'
annotateAnchors(dlo, features,
  featureName, maxgap = 1000)

## S4 method for signature 'loops,GRanges,character,numeric'
annotateAnchors(dlo, features,
  featureName, maxgap)

Arguments

dlo	A loops object whose anchors will be annotated
features	A Granges object corresponding to locations of interest
featureName	A string that will be the mcol name in anchors
maxgap	A value of max permissible gap between a feature and anchor

Details

This function adds column of TRUE/FALSE values on the loops object anchors whether a feature is observed nearby in features. The name of this column that will be in the anchors GRanges object is specified by a user defined string featureName. Gap tolerance between a feature and an anchor is specified by maxgap, where the default is 1,000bp.

Value

A loops object with new meta data column in anchors

Examples

# Annotate whether anchors are near a gene body; within 1kb
rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/')
load(rda)
gb <-getHumanGenes()
loops.small <- annotateAnchors(loops.small,gb,'nearGeneBody')

# Adding close to gene bodies with no gap tolerance
loops.small <- annotateAnchors(loops.small,gb,'inGeneBody',0)

aryeelab/diffloop documentation built on May 12, 2019, 3:42 a.m.