annotateAnchors.bed: Add meta data column to anchors based on bedgraph scores

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

Description

annotateAnchors.bed adds a numeric variable to meta data columns in the anchors slot based on a user-specified .bed file where the fourth column is a numeric score.

Usage

annotateAnchors.bed(dlo, file, FUN = mean, pad = 0)

## S4 method for signature 'ANY'
annotateAnchors.bed(dlo, file, FUN = mean, pad = 0)

Arguments

dlo	A loops object whose anchors will be annotated
file	A string pointing to the bed file of interest
FUN	A function used to combine multiple values observed in a single anchor; default is mean
pad	An integer value of to pad the anchors of the loops object; default is 0

Details

This function adds a meta data column to anchors of the specified loops object. All values from the .bed file that overlap with the each anchor are handled by the FUN (default is to average them) to produce a single value added to the mcols of the anchors.

Value

A loops object with new numeric 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')

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