configure: Configures the plates and plate result files

Description

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

Usage

## S3 method for class 'cellHTS':
configure(object, descripFile, confFile, logFile,
path, descFunArgs=NULL, confFunArgs=NULL, logFunArgs=NULL)

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. Alternatively this can be a function. See details.

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. Alternatively this can be a function. See details.

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. Alternatively this can be a function. See details.

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.

descFunArgs, confFunArgs, logFunArgs

optional; lists of additional arguments that can be passed on if one or more of descripFile, confFile or logFile are functions rather than file names. See details.

Value

An S4 object of class cellHTS, which is obtained by copying object and updating the following slots:
plateConfa data frame containing what was read from input file confFile (except the first two header rows).
screenLoga data frame containing what was read from input file logFile.
screenDescobject of class character containing what was read from input file descripFile.
statethe processing status of the cellHTS object is updated in to state["configured"]=TRUE.
featureDatathe column controlStatus is updated taking into account the well annotation given by the plate configuration file.
experimentDataan object of class MIAME containing descriptions of the experiment, constructed from the screen description file.

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.

Alternatively, any of the three arguments can also be a user-defined function returning data frames similar to those produced by read.table from the respective files. If confFile is a function, it has to return a list, where the first list item is an integer vector of length 2 giving the total number of plates and wells, and the second list item is the data.frame of the actual plate configuration. Additional parameters can be passed on to these functions via the descFunArgs, confFunArgs and logFunArgs arguments. This design allows for instance to import the necessary information directly from a data base rather than using flat files.

References

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

Examples

Run this code

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)

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