gff2RDList: Retrieve binding site information from GFF3 files.

In chroGPS: chroGPS2: Generation, visualization and differential analysis of epigenome maps

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]]

chroGPS documentation built on Oct. 31, 2019, 4:52 a.m.