gmap_build-methods

gmap_build,ANY,GmapGenome-method

gmap_build,character,GmapGenome-method

gmap_build,DNAStringSet,GmapGenome-method

destination directory for installation (defaults to gmapdb directory specified at configure time

k-mer value for genomic index (allowed: 12..15, default 14)

do not order chromosomes in numeric/alphabetic order, but use order in FASTA file(s)

files are gzipped, so need to gunzip each file first


  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. <a href="http://bioinformatics.oxfordjournals.org/content/26/7/873.abstract">Fast
    and SNP-tolerant detection of complex variants and splicing in short
    reads</a> offers an depth explication of IIT files and their use in GMAP and GSNAP. 


methods

 ~~ other possible keyword(s) ~~ 

GSNAP and GMAP are a pair of tools to align short-read
data written by Tom Wu.  This package provides convenience
methods to work with GMAP and GSNAP from within R. In addition,
it provides methods to tally alignment results on a
per-nucleotide basis using the bam_tally tool.

Michael Lawrence

gmapR

An R interface to the GMAP/GSNAP/GSTRUCT suite

gmap_build-methods function

<dl> <dt><code>signature(x = "ANY", genome = "GmapGenome")</code></dt><dd> </dd> <dt><code>signature(x = "character", genome = "GmapGenome")</code></dt><dd> </dd> <dt><code>signature(x = "DNAStringSet", genome = "GmapGenome")</code></dt><dd> </dd> </dl>

Methods

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. <href>http://bioinformatics.oxfordjournals.org/content/26/7/873.abstract</href>{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.

gmap_build-methods: Build Gmap/Gsnap Genome

Description

Arguments

Methods

Examples