makeGmapGenomePackage: Function to create a GmapGenome package from a GmapGenome...

Description Usage Arguments Author(s) See Also Examples

Description

A GmapGenome object is required to align reads using the GSNAP or GMAP algorithms. The makeGmapGenomePackage function allows users to save a particular GmapGenome object in an R package.

Usage

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makeGmapGenomePackage(gmapGenome, version, maintainer, author,
destDir = ".", license = "Artistic-2.0", pkgName)

Arguments

gmapGenome

A GmapGenome object.

version

The version number of this package.

maintainer

The maintainer of the package. The string must contain a valid email address.

author

The author of the package

destDir

The path that the new GmapGenome package should be created at.

license

The package's license (and its version)

pkgName

The name the package should have. Though free form, names of the form GmapGenome.Organism.Source.Build are recommended. E.g., GmapGenome.Hsapiens.UCSC.hg19

Author(s)

Cory Barr

See Also

GmapGenome

Examples

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## Not run: 
library(gmapR)

if (!require(BSgenome.Dmelanogaster.UCSC.dm3)) {
  library(BiocInstaller)
  biocLite("BSgenome.Dmelanogaster.UCSC.dm3")
  library(BSgenome.Dmelanogaster.UCSC.dm3)
}

gmapGenomePath <- file.path(getwd(), "flyGenome")
if (file.exists(gmapGenomePath)) unlink(gmapGenomePath, recursive=TRUE)
ggd <- GmapGenomeDirectory(gmapGenomePath, create = TRUE)
gmapGenome <- GmapGenome(genome=Dmelanogaster,
                         directory = ggd,
                         name = "dm3",
                         create = TRUE)

makeGmapGenomePackage(gmapGenome=gmapGenome,
                      version="0.1.0",
                      maintainer="<your.name@somewhere.com>",
                      author="Your Name",
                      destDir=".",
                      license="Artistic-2.0",
                      pkgName="GmapGenome.Dmelanogaster.UCSC.dm3")


## End(Not run)


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