chroGPS (version 1.16.0)

gff2RDList: 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 RangedDataList. 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 RangedDataList with the RangedData 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]]