xps (version 1.32.0)

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

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.

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).

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.

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)