makePDpackage {makePlatformDesign}R Documentation

Platform Design Package Maker

Description

This function creates the Platform Design package for Affymetrix and NimbleGen chips.

The objects generated by this package are soon going to be created by the pdInfoBuilder package.

For Affymetrix SNP arrays, use the pdInfoBuilder package.

Usage

makePDpackage(designFile, file1 = NULL, file2 = NULL,
              manufacturer = c("affymetrix", "nimblegen"),
              type = c("expression", "SNP", "tiling", "exon"),
              extra = NULL, genomebuild = "hg12")

Arguments

designFile a string with the name of the CDF/NDF file
file1 the FASTA/tab sequence file or the XYS file
file2 the annotation or *.POS file
manufacturer a choice between "affymetrix" or "nimblegen"
type array type: "expression", "SNP", "tiling" or "exon"
extra a list with several options for customization
genomebuild genome build information

Details

designFile is either a CDF or an NDF file, depending on the platform being used.

file1 is the FASTA sequence file if using an Affymetrix SNP Chip. It will be the tab-delimited sequence file if using an Affymetrix Expression Chip. If using a NimbleGen Chip, then it is an XYS file.

file2 is the annotation file for Affymetrix Chips or the *.POS file for NimbleGen Chips. Required for SNP Chips, optional otherwise.

extra is a list containing *all* the following elements: "packagename" (desired package name), "cdf.path" (path to the CDF), "package.path" (path where the package is to be saved), "author" (author of the package), "maintainer" (maintainer of the package), "version" (version of the package), "unlink" (boolean, deletes the package.path dir if it already exists), "verbose" (boolean).

Value

Either an affysnpBatch or an affyexprsBatch object, depending on the type of the array (SNP or expression).

Author(s)

Benilton Carvalho bcarvalh@jhsph.edu

See Also

writePackage

Examples

## NOT RUN
##
## -- Affymetrix Expression Chip --
## makePDpackage("CDF", "TAB-sequence-file", manufacturer="affymetrix",
##                type="expression")
##
## -- Affymetrix SNP Chip --
## makePDpackage("CDF", "FASTA", "ANNOT", manufacturer="affymetrix",
##                type="SNP")
##
## -- NimbleGen Expression Chip --
## makePDpackage("NDF", "XYS", "POS", manufacturer="nimblegen",
##                type="expression")


[Package makePlatformDesign version 1.0.0 Index]