relatePeaks {Ringo}R Documentation

Relate found peaks to genomic features

Description

This function relates found peaks to annotated genomic features, such as transcripts.

Usage

relatePeaks(pl, gff, upstream = 5000, verbose = TRUE)

Arguments

pl Object of class peakList
gff data.frame holding genomic feature annotation
upstream up to how many bases upstream of annotated genomic features should peaks be counted as related to that feature (see details)
verbose logical; extended output to STDOUT?

Details

Peaks will be counted as related to genomic features, if

.

One can visualize such peak-feature relations as a graph using the Bioconductor package Rgraphviz. See the script 'graphPeaks2Transcripts.R' in Ringo's scripts directory for an example.

Value

An object of class peakList with for each peak the elements typeUpstream and typeDownstream filled in with the names of the features that have been related to.

Author(s)

Joern Toedling toedling@ebi.ac.uk

Examples

  # see findPeaksOnSmoothed for an example

[Package Ringo version 1.2.0 Index]