readPlateList {cellHTS2} | R Documentation

## Read a collection of plate reader data files

### Description

Reads a collection of plate reader data files into a `cellHTS` object. The names of the files, plus additional information (plate number, repeat number, assay/treatment/condition) 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.
`name` | a character of length 1 with the experiment name.
`importFun` | a function to read the data files. The default function works for a certain file format, such as that of the example files provided with this package. If your plate reader software produces files with a different format, the import function needs to be adapted. See details.
`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 named `Filename`, `Plate`, and `Replicate`. The contents of the columns `Plate` and `Replicate` are expected to be integers. Further columns are allowed, and can be used to denote, for example, different variants of the assay, treatments, incubation times, conditions, etc.

`importFun` can be used to define a custom function to import data files. The `importFun` function should accept as its first argument names from the `Filename` column of the file table (which in principle do not need to be individual files, they could also be handles for database entries or pointers into relevants parts of a file). It should return a list with two components:

- The first component should be a `data.frame` with the following columns
  - `well`, a character vector with the well identifier in the plate.
  - `val`, the intensity values measured in that well.

  and with as many rows as there are wells in the plate.

- The second component 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 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 run 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` | information about the runs, infered from the `plateList` file: which replicate, which variant of the assay, treatment, incubation times etc.
`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 2.4.1 Index]