relateCERs: Relate found Chers to genomic features

In Ringo: R Investigation of ChIP-chip Oligoarrays

Description

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

Usage

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

• their middle position is located between start and end position of the feature

• their middle position is located not more than argument upstream bases upstream of the feature start

.

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

  # see findChersOnSmoothed for an example

Ringo documentation built on Nov. 8, 2020, 5:34 p.m.