GGtools (version 5.8.0)

gffprocess: transform a collection of gff3 into a single tabix-indexed gff3

Description

process a collection of gff3 into a single tabix-indexed gff3 using unix utilities to minimize memory requirements

Usage

gffprocess(basename = "fullyri100k", n_in = 44, headpatt = "_1A", tmpForSort = "/freshdata/tmp")

Arguments

basename

basename of the resulting .gff3.gz(.tbi) file

n_in

number of gff3 files to be processed -- used for consistency check against length(dir(patt="gff3"))

headpatt

pattern to identify file for the 'top' gff3 to be used as the contents are concatenated

tmpForSort

name of a folder that unix sort will use as a temporary directory

Value

Used for side effects. Will fail if any unix utility call via system() returns nonzero value. Returns NULL otherwise.

Details

The purpose of this utility is to exploit unix shell tools to unify a collection of gff3 files generated using link{All.cis}. The use case is cluster-based per-chromosome (or split chromosome) cis-testing generating a large number of GRanges that are transformed to gff3 to allow targeted interrogation.