gffprocess: transform a collection of gff3 into a single tabix-indexed...
In GGtools: software and data for analyses in genetics of gene expression

Description Usage Arguments Details Value Author(s)

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

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

`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

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.

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

VJ Carey <stvjc@channing.harvard.edu>

GGtools documentation built on Nov. 8, 2020, 6:32 p.m.