import.exon.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 Usage Arguments Details Value Warning Note Author(s) See Also Examples

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

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

`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.
`probeset`	name of probeset annotation-file, including full path.
`transcript`	name of transcript annotation-file, including full path.
`control`	optional name of controls.ps-file, including full path.
`add.mask`	logical. If `TRUE` mask information will be included as slot `mask`.
`verbose`	logical, if `TRUE` print status information.

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

A SchemeTreeSet object.

The current version of ‘xps’ should be able to import all Affymetrix exon array annotation files up to September 2011. However, since Affymetrix is still changing the headers and/or columns of the annotation files, future annotation files may require adaptation of the source code, thus the current version of ‘xps’ may not be able to read these files.

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.HuEx10stv2r2.na32" but use filename="Scheme_HuEx10stv2r2_na32" 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.

Christian Stratowa

import.expr.scheme, root.scheme, SchemeTreeSet

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

## create scheme for HuEx-1_0-st-v2.r2 Exon array
scheme.huex10stv2r2.na32 <- import.exon.scheme("Scheme_HuEx10stv2r2_na32", filedir=scmdir,
                            layoutfile=file.path(libdir, "HuEx-1_0-st-v2_libraryfile", "HuEx-1_0-st-r2/HuEx-1_0-st-v2.r2.clf"),
                            schemefile=file.path(libdir, "HuEx-1_0-st-v2_libraryfile", "HuEx-1_0-st-r2/HuEx-1_0-st-v2.r2.pgf"),
                            probeset=file.path(anndir, "HuEx-1_0-st-v2.na32.hg19.probeset.csv"),
                            transcript=file.path(anndir, "HuEx-1_0-st-v2.na32.hg19.transcript.csv"))

## access ROOT scheme file from new R session
scheme.exon <- root.scheme(paste(scmdir,"Scheme_HuEx10stv2r2_na32.root",sep="/"))


## create scheme for HuGene-1_0-st-v1.r4 as exon array
scheme.hugene10stv1r4.na32 <- import.exon.scheme("Scheme_HuGene10stv1r4_na32",filedir=scmdir,
                              layoutfile=file.path(libdir, "HuGene-1_0-st-v1.r4.analysis-lib-files", "HuGene-1_0-st-v1.r4.clf"),
                              schemefile=file.path(libdir, "HuGene-1_0-st-v1.r4.analysis-lib-files", "HuGene-1_0-st-v1.r4.pgf"),
                              probeset=file.path(anndir, "HuGene-1_0-st-v1.na32.hg19.probeset.csv"),
                              transcript=file.path(anndir, "HuGene-1_0-st-v1.na32.hg19.transcript.csv"))

## access ROOT scheme file from new R session
scheme.gene <- root.scheme(file.path(scmdir, "Scheme_HuGene10stv1r4_na32.root"))


## create scheme for HuEx-1_0-st-v2.r2 Exon array with the old annotation file
scheme.huex10stv2r2.old <- import.exon.scheme("Scheme_HuEx10stv2r2_old",filedir=scmdir,
                           layoutfile=file.path(libdir, "HuEx-1_0-st-v2_libraryfile", "HuEx-1_0-st-r2", "HuEx-1_0-st-v2.r2.clf"),
                           schemefile=file.path(libdir, "HuEx-1_0-st-v2_libraryfile", "HuEx-1_0-st-r2", "HuEx-1_0-st-v2.r2.pgf"),
                           probeset=file.path(anndir, "HuEx-1_0-st-probeset-annot.csv"),
                           transcript=file.path(anndir, "HuEx-1_0-st-transcript-annot.csv"),
                           control=file.path(libdir, "HuEx-1_0-st-v2_libraryfile", "HuEx-1_0-st-r2", "HuEx-1_0-st-v2.r2.controls.ps"))

## End(Not run)