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gmapR (version 1.14.0)

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

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

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

See Also

GmapGenome

Examples

Run this code
## 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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