makeLRBasePackage: Making LRBaseDb packages from corresponding table as single...

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/makeLRBasePackage.R

Description

makeLRBasePackage is a method that generates a package that will load an appropriate LRBaseDb object that will in turn point to existing annotation packages.

Usage

1
2
makeLRBasePackage(pkgname, data, metadata, organism, version,
    maintainer, author, destDir, license="Artistic-2.0")

Arguments

pkgname

The package name. We highly recommend that the name is ABC.XXX.eg.db-type, where ABC is some character and XXX is a abbreviation of organisms such as Hsa: Homo sapiens

data

Data frame contains Ligand GENEID (e.g., 100036770), Receptor GENEID (e.g., 100036770), SOURCEID (PMID), and SOURCEDB (e.g., FANTOM5)

metadata

Data frame contains metadata of the package

organism

The name of the organism this package represents

version

The version number of this package

maintainer

The maintainer who creates the package (must include email to be valid)

author

The creator of the package

destDir

A path where the package source should be assembled.

license

The license and it's version

Details

The purpose of this method is to create a special package that will depend on existing annotation packages and which will load a special LRBaseDb object that will allow proper dispatch of special select methods. These methods will allow the user to easily query across multiple annotation resources via information contained by the LRBaseDb object. Because the end result will be a package that treats all the data mapped together as a single source, the user is encouraged to take extra care to ensure that the different packages used are from the same build etc.

Value

A special package to load an LRBaseDb object.

Author(s)

Koki Tsuyuzaki

See Also

LRBaseDb

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
if(interactive()){
    ## makeLRBasePackage enable users to construct
    ## user's own custom LRBase package
    data(FANTOM5)
    head(FANTOM5)

    # We are also needed to prepare meta data as follows.
    data(metaFANTOM5)
    metaFANTOM5

    ## sets up a temporary directory for this example
    ## (users won't need to do this step)
    tmp <- tempfile()
    dir.create(tmp)

    ## makes an Organism package for human called Homo.sapiens
    makeLRBasePackage(pkgname = "FANTOM5.Hsa.eg.db",
        data = FANTOM5,
        metadata = metaFANTOM5,
        organism = "Homo sapiens",
        version = "0.99.0",
        maintainer = "Koki Tsuyuzaki <[email protected]>",
        author = "Koki Tsuyuzaki",
        destDir = tmp,
        license="Artistic-2.0")
}

LRBaseDbi documentation built on Nov. 1, 2018, 2:30 a.m.