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]