gff2RDList {chroGPS} | R Documentation

## Retrieve binding site information from GFF3 files.

### Description

An auxiliary function to retrieve binding site information from GFF3 format files (for instance those downloaded from modEncode, see function `getURL`).

### Usage

    gff2RDList(filenames,listnames,dir,quote=NULL,chrprefix='')

### Arguments

`filenames` | GFF3 filenames to read.
`listnames` | Names for each read filename, will be used as names of the returned `GRangesList`. If not given, filenames will be used as listnames.
`dir` | Directory where the GFF3 files are located.
`quote` | Quote character used in the GFF3 files around fields, if any.
`chrprefix` | Prefix to be placed before the chromosome names if desired, for instance 'chr'.

### Value

A list with Enriched and Depleted binding sites, each one is an object of class `GRangesList` with the `GRanges` objects containing the respective enriched or depleted binding sites from each GFF3 file.

### Examples

    # Not run
    #getURL('http://intermine.modencode.org/release-30/features.do?type=submission&action=export&format=gff3&submission=modENCODE_2984&feature=BindingSite&UCSC','test')
    #test <- gff2RDList('test.gff3',dir=getwd())
    #test
    #test$Enriched[[1]]
    #test$Depleted[[1]]

[Package chroGPS version 1.28.0 Index]