import.genome.scheme: Import CLF, PGF and annotation files into a SchemeTreeSet

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description

Import the Affymetrix CLF, PGF and transcript annotation files into a ROOT file and create S4 class SchemeTreeSet

Usage

import.genome.scheme(filename   = character(0),
                     filedir    = getwd(),
                     layoutfile = character(0),
                     schemefile = character(0),
                     transcript = character(0),
                     add.mask   = FALSE,
                     verbose    = TRUE)

Arguments

filename	file name of ROOT scheme file.
filedir	system directory where ROOT scheme file should be stored.
layoutfile	name of CLF-file, including full path.
schemefile	name of PGF-file, including full path.
transcript	name of transcript annotation-file, including full path.
add.mask	logical. If TRUE mask information will be included as slot mask.
verbose	logical, if TRUE print status information.

Details

import.genome.scheme is used to import all information for an Affymetrix whole genome array into a ROOT scheme file, including CLF and PGF-files, and the current Afymetrix transcript annotation files.

An S4 class SchemeTreeSet will be created, serving as R wrapper to the ROOT scheme file filename.

Since a new ROOT scheme file needs only to be created when new annotation files are available from the Affymetrix website, it is recommended to store all ROOT scheme files in a commonly accessible system directory filedir.

Use function root.scheme to access the ROOT scheme file from new R sessions to avoid creating a new ROOT scheme file for every session.

Value

A SchemeTreeSet object.

Warning

The current version of ‘xps’ is able to import all Affymetrix genome array annotation files up to November 2008, i.e. all files of release 3 (r3) and earlier. However, in January 2009 Affymetrix has updated all CLF, PGF and annotation files to release 4 (r4) and added a new probeset annotation file, thus in effect changing the whole genome arrays to exon arrays!

Thus, for release 4 (r4) files, function import.genome.scheme can no longer be used, but you must use function import.exon.scheme instead (see examples).

Note

As mentioned above, use function root.scheme to access the ROOT scheme file from new R sessions to avoid creating a new ROOT scheme file for every R session.

Do not separate filename of ROOT files with dots, use underscores, e.g. do not use filename="Scheme.HuGene10stv1.na27" but use filename="Scheme_HuGene10stv1_na27" instead. Extension “root” is added automatically, so that ROOT is able to recognize the file as ROOT file.

Do not set add.mask=TRUE unless you know that your computer has sufficient RAM.

Do not add item control unless you want to use one of the old annotation files where the probeset annotation file does not contain the AFFX controls.

Author(s)

Christian Stratowa

See Also

import.exon.scheme, root.scheme, SchemeTreeSet

Examples

## Not run: 
## define paths
scmdir <- "/common/path/schemes"
libdir <- "/my/path/Affy/libraryfiles"
anndir <- "/my/path/Affy/Annotation"

## create scheme for HuGene-1_0-st-v1 whole genome array
scheme.hugene10stv1r3.na27 <- import.genome.scheme("Scheme_HuEx10stv1r3_na27", filedir=scmdir,
                              layoutfile=file.path(libdir, "HuGene-1_0-st-v1.r3.analysis_libraryfile", "HuGene-1_0-st-v1.r3.clf"),
                              schemefile=file.path(libdir, "HuGene-1_0-st-v1.r3.analysis_libraryfile", "HuGene-1_0-st-v1.r3.pgf"),
                              transcript=file.path(anndir, "HuGene-1_0-st-v1.na27.hg18.transcript.csv"))

## access ROOT scheme file from new R session
scheme.hugene10stv1r3 <- root.scheme(file.path(scmdir, "Scheme_HuEx10stv1r3_na27.root"))

## End(Not run)

xps documentation built on Nov. 8, 2020, 6 p.m.