InstallBrainArrayPackage: Helper function for installing BrainArray packages

Description Usage Arguments Value Note Author(s) Examples

View source: R/Helper.R

Description

When processing Affymetrix microarrays, users can specify alternative probe/gene mappings via the probeSummaryPackage parameter. Users can download such packages directly from the BrainArray web site and install them manually. Or they can use this helper function to download and install them in a single step.

Usage

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InstallBrainArrayPackage(celFilePath, version, organism, annotationSource)

Arguments

celFilePath

Path to an example CEL file. The Affymetrix version name will be extracted from this file.

version

Version of BrainArray (for example, "17.1.0") you want to download.

organism

Abbreviated name (for example, "hs" = homo sapiens, "mm" = mus musculus, "gg" = gallus gallus) of the organism for which the microarrays are designed.

annotationSource

Abbreviated name of the annotation source (for example, "entrezg" = Entrez Gene, "ensg" = Ensembl Gene) you want to use.

Value

A character object that indicates the name of the installed package.

Note

Information about BrainArray versions, organism names, and annotation sources can be obtained via the BrainArray web site (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp).

Author(s)

Stephen R. Piccolo

Examples

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## Not run: 
pkgName = InstallBrainArrayPackage(celFilePath, "17.0.1", "hs", "entrezg")

## End(Not run)

SCAN.UPC documentation built on Nov. 17, 2017, 11:17 a.m.