GSTRUCT suite

Description Usage Arguments Author(s) See Also Examples

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.

1 2	makeGmapGenomePackage(gmapGenome, version, maintainer, author, destDir = ".", license = "Artistic-2.0", pkgName)

`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

Cory Barr

GmapGenome

## Not run: 
library(gmapR)

if (!require(BSgenome.Dmelanogaster.UCSC.dm3)) {
  library(BiocManager)
  BiocManager::install("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)