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, importFun, verbose=TRUE, plateType)

### 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`.
`importFun` | a function that should be used to read each plate result file. The default function works for plate reader data files. See details.
`verbose` | a logical value, if TRUE, the function reports some of its intermediate progress.
`plateType` | (deprecated argument) a character of length 1 giving the format of the plate: "96" for 96-well plate format, or "384" for a 384-well plate format.

### 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.

`importFun` can be used to define other functions to import other data files, such as flow cytometry data files, etc. The `importFun` function should receive as an input the name of a result plate file to read, and return a list with two components:

- The first component should be a 'data.frame' with the following slots:
  - `well`, a character vector with the well identifier in the plate.
  - `val`, the intensity values measured at each well.
- The second component of this list should be a character vector containing a copy of the imported input data file (such as the output of `readLines`). It should be suitable to be used as input for `writeLines`, since it will be used to reproduce the intensity files that are linked in the HTML quality reports generated by `writeReport`.

For example, to import plate data files from EnVision plate reader, set `importFun=getEnVisionRawData` or `importFun=getEnvisionCrosstalkCorrectedData`. See function `getEnVisionRawData`.

### 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, containing the imported measurement data.
`pdim` | a numeric vector of length 2 containing the number of rows and columns in a plate. The product of these two numbers is the first dimension of `xraw`. This corresponds to the plate format used in the screen, and it is automatically determined from the plate result files. The allowed formats are 96-well or 384-well plates.
`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, where each component contains 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, Ligia Braz ligia@ebi.ac.uk

### See Also

`getEnVisionRawData`

### Examples

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

        ## To read data files obtained from an EnVision plate reader:
        datadir <- system.file("EnVisionExample", package = "cellHTS")
        x <- readPlateData("platelist.txt", "EnVisionEx",
              importFun=getEnVisionRawData, path=datadir)

           ## to get the cross talk corrected data:
           y <- readPlateData("platelist.txt", "EnVisionEx",
               importFun=getEnVisionCrosstalkCorrectedData, path=datadir)

[Package cellHTS version 1.10.0 Index]