readPlateData {cellHTS} | R Documentation

## Read a collection of plate reader data files

### Description

Reads a collection of plate reader data files into a data.frame. The names of the files, plus additional information (plate number, repeat number) is expected in a tab-delimited table specified by the argument 'x'.

### Usage

    readPlateData(filename, path=dirname(filename), name, plateType="384", verbose=TRUE)

### Arguments

`filename` | the name of the file table (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.
`name` | a character of length 1 with the experiment name.
`path` | a character of length 1 indicating the path in which to find the plate reader files. By default, it can extract the path from `filename`.
`plateType` | a character of length 1, allowed values are "96" and "384".
`verbose` | a logical value, if TRUE, the function reports some of its intermediate progress.

### Details

The file table is expected to be a tab-delimited file with at least three columns, and column names `Filename`, `Plate`, and `Replicate`. The contents of the columns `Plate` and `Replicate` are expected to be integers. Further columns are allowed.

We distinguish between plates and plate result file. A plate result file contains the measurements results for all replicates and all channels of a plate, which is the physical carrier of the reagents.

### Value

An object of class `"cellHTS"`, which is currently implemented as a list with elements

`name` | copy of the input argument `name`
`xraw` | an array of dimension plateSize x number of plates x number of replicates x number of channels, containg the imported measurement data.
`pdim` | a numeric vector of length 2 containg the number of rows and columns in a plate. The product of these two numbers is the first dimension of `xraw`.
`batch` | an integer vector with the batch number (1, 2, ...) for each plate. Its length corresponds to the second dimension of of `xraw`.
`plateList` | a data.frame containing what was read from input file `x`, plus a column `status` of type character: it contains the string "OK" if the data import appeared to have gone well, and the respective error or warning message otherwise.
`intensityFiles` | a list of character vectors, each containing a copy of the imported input data files. Its length corresponds to the number of rows of `plateList`.
`state` | a logical vector representing the processing status of the object.

### Author(s)

W. Huber huber@ebi.ac.uk

### References

..

### Examples

     datadir = system.file("KcViabSmall", package = "cellHTS")
     x = readPlateData("Platelist.txt", "KcViabSmall", path=datadir)

[Package cellHTS version 1.2.0 Index]