configure {cellHTS} | R Documentation

## Configures the plates and plate result files

### Description

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

### Usage

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

### Arguments

`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.
`...` | additional parameters - ignored.

### Details

confFile
  This 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.
logFile
  If 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.
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 `x` in slot `xraw`.

### Value

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`.
`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`.

### Author(s)

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

### References

..

### Examples

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

[Package cellHTS version 1.6.0 Index]