| import.genome.scheme {xps} | R Documentation |
Import the Affymetrix CLF, PGF and transcript annotation files into a ROOT file and create S4 class SchemeTreeSet
import.genome.scheme(filename = character(0),
filedir = getwd(),
layoutfile = character(0),
schemefile = character(0),
transcript = character(0),
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. |
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. |
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.
A SchemeTreeSet object.
The current version of ‘xps’ should be able to import all Affymetrix genome array annotation files up to July 2007. 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.HuGene10stv1.na23" but use filename="Scheme_HuGene10stv1_na23"
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.exon.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 HuGene-1_0-st-v1 whole genome array
scheme.hugene10stv1r3.na23 <- import.genome.scheme("Scheme_HuEx10stv1r3_na23",filedir=scmdir,
layoutfile=paste(libdir,"HuGene-1_0-st-v1.r3.analysis_libraryfile/HuGene-1_0-st-v1.r3.clf",sep="/"),
schemefile=paste(libdir,"HuGene-1_0-st-v1.r3.analysis_libraryfile/HuGene-1_0-st-v1.r3.pgf",sep="/"),
transcript=paste(anndir,"HuGene-1_0-st-v1.na23.hg18.transcript.csv",sep="/"))
## access ROOT scheme file from new R session
scheme.hugene10stv1r3 <- root.scheme(paste(scmdir,"Scheme_HuEx10stv1r3_na23.root",sep="/"))
## End(Not run)