configure: Configures the plates and plate result files
In cellHTS: Analysis of cell-based screens

Description Usage Arguments Details Value Author(s) References See Also Examples

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

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configure(x, ...)
## S3 method for class 'cellHTS'
configure(x, confFile, logFile, descripFile, path, ...)

`x`	a `cellHTS` object.
`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.
`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.
`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.
`...`	additional parameters - ignored.

confFileThis file is expected to be a tab-delimited file with at least three columns, and column names Batch, Well and Content. The contents of Batch are expected to be integer.
logFileIf given as an argument, it is expected to be a tab-delimited file with at least three columns, and column names Filename, Well, and Flag. Further columns are allowed.
descripFileThis 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 x in slot xraw.

An S3 object of class cellHTS, which extends the argument x by the following elements:

`plateConf`	a data.frame containing what was read from input file `confFile`. The number of rows is equal to the product between the number of wells in each plate and the number of batches.
`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`.

Moreover, the processing status of the cellHTS object is updated in the slot state to state["configured"]=TRUE.

wellAnno

object of class factor of length number of plates x number of wells per plate, with possible levels: empty, other, neg, sample, and pos, indicative of the contents of the wells. Other levels may be employed for the positive and negative controls, besides pos and neg.

There are methods print.cellHTS, configure.cellHTS and annotate.cellHTS.

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

readPlateData

## Not run: 
    datadir <- system.file("KcViabSmall", package = "cellHTS")
    x <- readPlateData("Platelist.txt", "KcViabSmall", path=datadir)
    x <- configure(x, "Plateconf.txt", "Screenlog.txt", "Description.txt", path=datadir)

## End(Not run)