| import.data {xps} | R Documentation |
Import the Affymetrix CEL files into a ROOT file and create S4 class DataTreeSet
import.data(xps.scheme,
filename = character(0),
filedir = getwd(),
celdir = NULL,
celfiles = "*",
celnames = NULL,
project = NULL,
verbose = TRUE)
xps.scheme |
a SchemeTreeSet containing the correct scheme for the CEL-files |
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 ProjectInfo. |
verbose |
logical, if TRUE print status information. |
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.
Currently, the following types of Affymetrix CEL-files can be imported: text, xml, binary (xda), generic (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.
Christian Stratowa
## 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))