import.expr.scheme {xps} | R Documentation |
Import the Affymetrix CDF, probe and annotation files into a ROOT file and create S4 class SchemeTreeSet
import.expr.scheme(filename = character(0), filedir = getwd(), schemefile = character(0), probefile = character(0), annotfile = character(0), chipname = NULL, add.mask = FALSE, verbose = TRUE)
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. |
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.
A SchemeTreeSet
object.
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.Test3.na27"
but use filename="Scheme_Test3_na27"
or simply
filename="SchemeTest3na27"
instead. Extension “root” is added automatically,
so that ROOT is able to recognize the file as ROOT file.
For a few probesets, parsing the Affymetrix annotation files will provide ambiguous results.
Setting verbose=11
will list these probesets.
Christian Stratowa
import.exon.scheme
, import.genome.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 Test3 GeneChip scheme.test3.na27 <- import.expr.scheme("Scheme_Test3_na27",filedir=scmdir, schemefile=paste(libdir,"Test3.CDF",sep="/"), probefile=paste(libdir,"Test3_probe.tab",sep="/"), annotfile=paste(anndir,"Test3.na27.annot.csv",sep="/")) ## access ROOT scheme file from new R session scheme.test3 <- root.scheme(paste(scmdir,"Scheme_Test3_na27.root",sep="/")) ## create scheme for HG-U133_Plus_2 GeneChip scheme.hgu133p2.na27 <- import.expr.scheme("Scheme_HGU133p2_na27",filedir=scmdir, schemefile=paste(libdir,"HG-U133_Plus_2.cdf",sep="/"), probefile=paste(libdir,"HG-U133-PLUS_probe.tab",sep="/"), annotfile=paste(anndir,"HG-U133_Plus_2.na27.annot.csv",sep="/")) ## access ROOT scheme file from new R session scheme.hgu133p2 <- root.scheme(paste(scmdir,"Scheme_HGU133p2_na27.root",sep="/")) ## End(Not run)