import.data {xps}R Documentation

Import CEL files into a DataTreeSet

Description

Import the Affymetrix CEL files into a ROOT file and create S4 class DataTreeSet

Usage

import.data(xps.scheme,
            filename = character(0),
            filedir  = getwd(),
            celdir   = NULL,
            celfiles = "*",
            celnames = NULL,
            project  = NULL,
            verbose  = TRUE)

Arguments

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.

Details

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.

Value

A DataTreeSet object.

Note

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.

Author(s)

Christian Stratowa

See Also

root.data, DataTreeSet

Examples

## 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))

[Package xps version 1.0.2 Index]