readPlateList {cellHTS2} | R Documentation |
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
.
readPlateList(filename, path=dirname(filename), name, importFun, verbose=interactive())
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() . |
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:
well
, a character vector with the well identifier in the plate.
val
, the intensity values measured at each well.
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
.
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 . |
W. Huber huber@ebi.ac.uk, Ligia Bras ligia@ebi.ac.uk
Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of cell-based RNAi screens, Genome Biology 7, R66.
To read input files obtained in a HTanalyser plate reader see readHTAnalystData
.
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)