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:

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 2.6.0 Index]