readPlateList {cellHTS2} | 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 `filename`.

### Usage

    readPlateList(filename, path=dirname(filename), name, importFun, verbose=interactive())

### 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.
`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`.
`name` | a character of length 1 with the experiment name.
`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. Defaults to the state of `interactive()`.

### 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`.

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 extends the class `NChannelSet`. After calling this function, the content of the following slots is as follows:

`assayData` | an object of class `AssayData` containing the imported measurement data. Each matrix represents a single channel, and each sample (replicate) corresponds to a column. Thus, the total number of rows in each matrix corresponds to the product between the number of wells per plate and the number of assay plates.
`phenoData` | the argument `name` is stored in its column `assay`.
`featureData` | the information about the plate and well identifiers for each plate measurement are stored in columns `plate` and `well` of this slot.
`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`.

### Author(s)

W. 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

To read input files obtained in a HTanalyser plate reader see `readHTAnalystData`.

### Examples

        datadir <- system.file("KcViabSmall", package = "cellHTS2")
        x <- readPlateList("Platelist.txt", "KcViabSmall", path=datadir)

       ## To read data files obtained from an EnVision plate reader:
        datadir <- system.file("EnVisionExample", package = "cellHTS2")
        x <- readPlateList("platelist.txt", name="EnVisionEx",
              importFun=getEnVisionRawData, path=datadir)

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

[Package cellHTS2 version 2.2.5 Index]