xps (version 1.32.0)

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

Description

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

Usage

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)

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.

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.

Value

A SchemeTreeSet object.

Warning

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.

Details

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.

See Also

import.expr.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 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)