relateCERs: Relate found Chers to genomic features

Description Usage Arguments Details Value Author(s) Examples

Description

This function relates found 'cher's (ChIP-enriched regions) to annotated genomic features, such as transcripts.

Usage

1
relateChers(pl, gff, upstream = 5000, verbose = TRUE)

Arguments

pl

Object of class cherList

gff

data.frame holding genomic feature annotation

upstream

up to how many bases upstream of annotated genomic features should chers be counted as related to that feature (see details)

verbose

logical; extended output to STDOUT?

Details

chers will be counted as related to genomic features, if

.

One can visualize such cher-feature relations as a graph using the Bioconductor package Rgraphviz. See the script 'graphChers2Transcripts.R' in Ringo's scripts directory for an example.

Value

An object of class cherList with for each cher the elements typeUpstream and typeInside filled in with the names of the features that have been related to.

Author(s)

Joern Toedling

Examples

1
  # see findChersOnSmoothed for an example

Ringo documentation built on Nov. 1, 2018, 3:44 a.m.