xps (version 1.32.0)

import.data: 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.

Value

A DataTreeSet object.

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.

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.

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))