relateChers {Ringo} | R Documentation

## Relate found Chers to genomic features

### 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

[Package Ringo version 1.44.0 Index]