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gmapR (version 1.10.0)

An R interface to the GMAP/GSNAP/GSTRUCT suite

Description

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.

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Version

Version

1.10.0

License

Artistic-2.0

Maintainer

Michael Lawrence

Last Published

February 15th, 2017

Functions in gmapR (1.10.0)

Align a Set of Reads Using the GSNAP Aligner

GsnapParam-class

Class "GsnapParam"

gmapR2 internals

GsnapOutput-class

Class "GsnapOutput"

bam_tally-methods

Per-position Alignment Summaries

BamTallyParam-class

Class "BamTallyParam"

GmapGenome-class

Class "GmapGenome"

GmapGenomeDirectory-class

Class "GmapGenomeDirectory"

makeGmapGenomePackage

Function to create a GmapGenome package from a GmapGenome object

Demo genome around TP53

Get the Path to the Location on Disk from a gmapR Class

gmap_build-methods

Build Gmap/Gsnap Genome

GmapSnpDirectory-class

Class "GmapSnpDirectory"

Class "GmapSnps"