makeChipPackageFromDataFrames: Making a chip package from annotations available from...

In Bioconductor/AnnotationForge: Tools for building SQLite-based annotation data packages

Making a chip package from annotations available from data.frame of probes mapped to gene IDs and an existing org package.

Description

The makeChipPackage function allows the user to make an chip package from a data.frame that has two columns to define a set of probes and the gene IDs that they map to as well as an org package that contains data about those gene IDs (where the gene IDs can be used as a foreign key).

makeChipPackage is intended to be compatible with any org packages that are generated by makeOrgPackage as well as most of the older legacy org packages that were based on more popular model organisms. The one exception is the legacy org package for yeast org.Sc.sgd.db since its internal schema is just too different from everything else.

Packages produced in this way can not support the older bimap objects unless they are pointing to an older legacy org package. All packages should support select().

Usage

  makeChipPackage(prefix,
                  probeFrame, 
                  orgPkgName, 
                  version,
                  maintainer,
                  author,
                  outputDir = ".",
                  tax_id,
                  genus,
                  species,
                  optionalAccessionsFrame=NULL)

Arguments

prefix	The package name
probeFrame	data.frame with two columns. The 1st column are the probes and the second column are genes (gene IDs). The gene IDs must be the main ID type for the org package that is the named in the 3rd argument.
orgPkgName	The name of the org package that you want to make the chip package to go with
version	What is the version number for this package? format: \'x.y.z\'
maintainer	Who is the package maintainer? (must include email to be valid)
author	Who is the creator of this package?
outputDir	A path where the package source should be assembled.
tax_id	The Taxonomy ID that represents your organism. (NCBI has a nice online browser for finding the one you need)
genus	Single string indicating the genus.
species	Single string indicating the species.
optionalAccessionsFrame	If you want to also include accessions for your probes (not used for mapping them) then you can include those here.

Value

The path to the package that just created. This is useful for calling install.packages as the next step.

Author(s)

M. Carlson

Examples

if(interactive()){
## 1st lets list some authentic entrez gene IDs
geneIds <- c("1","10","100","1000","10000","100008586")
probeNames <- paste("probe", 1:length(geneIds), sep="")
probeFrame <- data.frame(probes=probeNames, genes=geneIds)

makeChipPackage(prefix='testChip',
                probeFrame=probeFrame,
                orgPkgName='org.Hs.eg.db',
                version='0.99.1',
                maintainer='Some One <[e-mail]>',
                author='Some One <[e-mail]>',
                outputDir='.',
                tax_id='59729',
                genus='Homo',
                species='sapiens')

## then you can call install.packages based on the return value
install.packages('./testChip.db', repos=NULL)

}

Bioconductor/AnnotationForge documentation built on Nov. 2, 2024, 6:30 a.m.