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. The optional `Batch` column can be used to supply batch information for an experiment, e.g., when a reagent has been changed or the experiment has been run over several days.

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, Florian Hahne

### 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 2.8.3 Index]