import.expr.scheme: Import CDF, probe 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 CDF, probe and annotation files into a ROOT file and create S4 class SchemeTreeSet

Usage

import.expr.scheme(filename   = character(0),
                   filedir    = getwd(),
                   schemefile = character(0),
                   probefile  = character(0),
                   annotfile  = character(0),
                   chipname   = NULL,
                   add.mask   = FALSE,
                   verbose    = TRUE)

Arguments

filename	file name of ROOT scheme file.
filedir	system directory where ROOT scheme file should be stored.
schemefile	name of CDF-file, including full path.
probefile	name of probe-file, including full path.
annotfile	name of annotation-file, including full path.
chipname	optional chip name when using an alternative CDF-file.
add.mask	logical. If TRUE mask information will be included as slot mask.
verbose	logical, if TRUE print status information.

Details

import.expr.scheme is used to import all information for an Affymetrix expression array into a ROOT scheme file, including CDF-file, the corresponding probe file, and the current Afymetrix annotation file.

Usually, chipname is extracted from the name of the CDF-file, however, when using an alternative CDF-file, e.g. from BrainArray or AffyProbeMiner, a chipname must be supplied which starts with (or contains) the exact Affymetrix chip name.

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 a new annotation file is 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.

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.Test3.na32" but use filename="Scheme_Test3_na32" or simply filename="SchemeTest3na32" instead. Extension “root” is added automatically, so that ROOT is able to recognize the file as ROOT file.

For a few probesets, parsing the Affymetrix annotation files will provide ambiguous results. Setting verbose=11 will list these probesets.

Author(s)

Christian Stratowa

See Also

import.exon.scheme, import.genome.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 Test3 GeneChip
scheme.test3.na32 <- import.expr.scheme("Scheme_Test3_na32", filedir=scmdir,
                     schemefile=file.path(libdir, "Test3.CDF"),
                     probefile=file.path(libdir, "Test3_probe.tab"),
                     annotfile=file.path(anndir, "Test3.na32.annot.csv"))

## access ROOT scheme file from new R session
scheme.test3 <- root.scheme(file.path(scmdir, "Scheme_Test3_na32.root"))


## create scheme for HG-U133_Plus_2 GeneChip
scheme.hgu133p2.na32 <- import.expr.scheme("Scheme_HGU133p2_na32", filedir=scmdir,
                        schemefile=file.path(libdir, "HG-U133_Plus_2.cdf"),
                        probefile=file.path(libdir, "HG-U133-PLUS_probe.tab"),
                        annotfile=file.path(anndir, "HG-U133_Plus_2.na32.annot.csv"))

## access ROOT scheme file from new R session
scheme.hgu133p2 <- root.scheme(file.path(scmdir, "Scheme_HGU133p2_na32.root"))

## End(Not run)

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