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, plateType="384", verbose=TRUE)

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.
plateType a character of length 1, allowed values are "96" and "384".
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, 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.

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, containg the imported measurement data.
pdim a numeric vector of length 2 containg the number of rows and columns in a plate. The product of these two numbers is the first dimension of xraw.
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 of character vectors, each containing 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

References

..

Examples

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

[Package cellHTS version 1.2.0 Index]