gmap_build-methods: Build Gmap/Gsnap Genome

In gmapR: An R interface to the GMAP/GSNAP/GSTRUCT suite

Description

Construct the IIT (interval index tree) needed from the GMAP suite of tools to run from a genome file. IIT files are an oligomer index and what allow GMAP and GSNAP to efficiently lookup interval information for fast genomic mapping. Fast and SNP-tolerant detection of complex variants and splicing in short reads offers an depth explication of IIT files and their use in GMAP and GSNAP.

Arguments

d	genome name
D	destination directory for installation (defaults to gmapdb directory specified at configure time
k	k-mer value for genomic index (allowed: 12..15, default 14)
S	do not order chromosomes in numeric/alphabetic order, but use order in FASTA file(s)
g	files are gzipped, so need to gunzip each file first

Methods

signature(x = "ANY", genome = "GmapGenome")

signature(x = "character", genome = "GmapGenome")

signature(x = "DNAStringSet", genome = "GmapGenome")

Examples

## Not run: flyGG <- GmapGenome(genome = "dm3",
                    directory = ggd)
gmap_build(x=Dmelanogaster, genome=flyGG)

## End(Not run)

gmapR documentation built on Nov. 8, 2020, 5:29 p.m.