configure {cellHTS2}R Documentation

Configures the plates and plate result files

Description

Annotate the plates and the plate result files of a cellHTS object.

Usage

## S4 method for signature 'cellHTS':
configure(object, descripFile, confFile, logFile, path)

Arguments

object a cellHTS object.
descripFile the name of the screen description file (see details). This argument is just passed on to the readLines function, so any of the valid argument types for readLines are valid here, too.
confFile the name of the configuration file (see details). This argument is just passed on to the read.table function, so any of the valid argument types for read.table are valid here, too. Must contain one row for each well and each batch.
logFile optional; the name of the screen log file (see details). This argument is just passed on to the read.table function, so any of the valid argument types for read.table are valid here, too.
path optional; a character of length one indicating the path in which to find the configuration files. It can be useful when the files are located in the same directory, and may be omitted otherwise.

Details

The configuration has three components:

confFile: This file specifies where the controls are. This file is expected to be a tab-delimited file with two first header rows giving the total number of wells and plates in the screen. The next rows should be in the form of a spreadsheet table with at least three columns named Plate, Well and Content. Columns Plate and Well are allowed to contain regular expressions. Data from wells that are configured as empty will be ignored and are set to NA in the data slot xraw. For an example, and for more details, please read the accompanying vignette.

logFile: This optional file allows to flag certain measurements as invalid. It is expected to be a tab-delimited file with at least three columns, and column names Plate, Well, and Flag. If there are multiple samples (replicates or conditions), a column called Sample should also be given. If there are multiple channels, a column called Channel must be given. Further columns are allowed.

descripFile: The screen description file contains general information about the screen.

Value

An S4 object of class cellHTS, which is obtained by copying object and updating the following slots:

plateConf a data frame containing what was read from input file confFile (except the first two header rows).
screenLog a data frame containing what was read from input file logFile.
screenDesc object of class character containing what was read from input file descripFile.
state the processing status of the cellHTS object is updated in to state["configured"]=TRUE.
featureData the column controlStatus is updated taking into account the well annotation given by the plate configuration file.
experimentData an object of class MIAME containing descriptions of the experiment, constructed from the screen description file.

Author(s)

Wolfgang Huber huber@ebi.ac.uk, Ligia Bras ligia@ebi.ac.uk

References

Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of cell-based RNAi screens, Genome Biology 7, R66.

See Also

readPlateList templateDescriptionFile

Examples


    datadir <- system.file("KcViabSmall", package = "cellHTS2")
    x <- readPlateList("Platelist.txt", name="KcViabSmall", path=datadir)
    x <- configure(x, "Description.txt", "Plateconf.txt", "Screenlog.txt", path=datadir)

[Package cellHTS2 version 2.6.0 Index]