configure {cellHTS2}R Documentation

Configures the plates and plate result files

Description

Annotate the plates and the plate result files of a given 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. Useful when the files are locate in the same directory, but should be omitted otherwise.

Details

confFile
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 data.frame with at least three columns named Plate, Well and Content. Columns Plate and Well are allowed to contain regular expressions. For more details about the plate configuration file, read the accompanying vignette.
logFile
If given as an argument, 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
This file is the screen description file with general information about the screen.

Data from wells that are annotated as empty are ignored and are set to NA in object in slot xraw.

Value

An S4 object of class cellHTS, which extends the class NChannelSet. The followings slots of object are updated:

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 having 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

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 2.2.5 Index]