annotateAnchors.bed {diffloop} | R Documentation

## Add meta data column to anchors based on bedgraph scores

### 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')

[Package diffloop version 1.8.0 Index]