import.data: Import CEL files into a DataTreeSet

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

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.

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.

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.

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.

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))

xps documentation built on Nov. 8, 2020, 6 p.m.