xps (version 1.32.0)

import.expr.scheme: Import CDF, probe and annotation files into a SchemeTreeSet

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.

Value

A SchemeTreeSet object.

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.

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)