Description Usage Arguments Details Value Note Author(s) See Also Examples
Import the Affymetrix CEL files into a ROOT file and create S4 class DataTreeSet
1 2 3 4 5 6 7 8 |
xps.scheme |
a |
filename |
file name of ROOT data file. |
filedir |
system directory where ROOT data file should be stored. |
celdir |
system directory containing the CEL-files for corresponding scheme. |
celfiles |
optional vector of CEL-files to be imported. |
celnames |
optional vector of names which should replace the CEL-file names. |
project |
optional class |
verbose |
logical, if |
import.data
is used to import CEL-files from directory celdir
into
a ROOT
data file. To import only a subset of CEL-files, list these CEL-files
as vector celfiles
.
To import CEL-files from different directories, vector celfiles
must contain the
full path for each CEL-file and celdir
must be celdir=NULL
.
The optional parameter celnames
allows you to replace the original CEL-file names with
names of your choice, otherwise the names of the CEL-files will be used as celnames
.
Currently, the following types of Affymetrix CEL-files can be imported: text (version 3), xml, binary (xda), generic (agcc,calvin)
An S4 class DataTreeSet
will be created, serving as R wrapper to the
ROOT
data file filename
.
Use function root.data
to access the ROOT
data file from new
R sessions to avoid creating a new ROOT
data file for every session.
A DataTreeSet
object.
As mentioned above, use function root.data
to access the
ROOT data file from new R sessions to avoid creating a new ROOT
data file
for every R session.
Do not separate filename
of ROOT files with dots, use underscores, e.g. do not use
filename="Data.Test3"
but use filename="Data_Test3"
or filename="DataTest3"
instead.
To every ROOT data file the extension “\_cel” is attached to filename
to easily
recognize ROOT data files containing the raw CEL data, e.g. for filename="Data_Test3"
the final name is “Data\_Test3\_cel.root”. Extension “root” is added automatically,
so that ROOT is able to recognize the file as ROOT file.
Once a ROOT
file is created it can not be overwritten, it must be deleted
manually first. Only ROOT
files called “tmp” or with filename
starting with “tmp\_” will be re-created automatically.
If CEL-file names contain dots, colons, parenthesis, etc. as characters, these characters will be
replaced by underscores. It is recommended to use parameter celnames
to create shorter CEL
names and to replace special characters.
Christian Stratowa
1 2 3 4 5 6 7 8 9 | ## get scheme and import CEL-files from package
scheme.test3 <- root.scheme(paste(path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
data.test3 <- import.data(scheme.test3,"tmp_data_test3",celdir=paste(path.package("xps"),"raw",sep="/"))
unlist(treeNames(data.test3))
## import only subset of CEL-files
subdata.test3 <- import.data(scheme.test3,"tmpdt_data_test3",celdir=paste(path.package("xps"),"raw",sep="/"),
celfiles=c("TestA1.CEL","TestB2.CEL"),verbose=FALSE)
unlist(treeNames(subdata.test3))
|
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