gffprocess {GGtools} | R Documentation

## 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

### 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.

### Value

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

### Author(s)

VJ Carey <stvjc@channing.harvard.edu>

[Package GGtools version 5.22.0 Index]