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, 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.

### 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.

### 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 2.46.1 Index]