Reads a collection of plate reader data files into a
object. The names of the files, plus additional information (plate
number, repeat number, assay/treatment/condition) is expected to be
stored in a tab-delimited table specified by the argument
filename. Alternatively, the data can be provided directly from
non file-based sources, e.g. a data base (see details).
the name of the plate list file (see details). This
argument is just passed on to the
a character of length 1 indicating the path in which to
find the plate reader files. If the
a character of length 1 with the experiment name.
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 or if you want to import data from a non file-based source, the import function needs to be adapted. See details and examples.
Optional argument that is passed to importFun, and can be
used to accommodate for data files that use characters different
a logical value, if TRUE, the function reports some of its intermediate progress.
additional arguments that are being passed on to
The plate list is expected to be a tab-delimited file with at least
three columns named
Replicate. The contents of the columns
Replicate are expected to be integers.
be a vector of file names of the respective raw data files. If the
path argument is supplied and
importFun is missing, its
value will automatically be prepended to the file names. 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.
Alternatively, the value of
filename can be a user-defined
function which creates a
data.frame similar to the one
described before. This is for instance useful if the plate list
information is directly imported from a data base. In order to allow
for non-elementary data types, the output of the function can also be
a named list, where each element has to be a vector of equal
length. The aforementioned type restrictions still apply. The function
will be called with all additional ... arguments, which allows to
pass in additional information like experiment identifiers or data
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 plate list
(which in principle do not need to be individual files, they could
also be handles for database entries, queries, or pointers into
relevants parts of a file). As it second argument, the function should
accept the value of the
path argument, and the user needs to
explicitely prepend this to the file names if needed. It should return
a list with two components:
The first component should be a
data.frame with the
well, a character vector with the well identifier in
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
since it will be used to reproduce the intensity files that are
linked in the HTML quality reports generated by
For example, to import plate data files from EnVision plate reader,
importFun=getEnvisionCrosstalkCorrectedData. See function
Direct data base import without the need for any flat files at all could for instance be achieved by:
Providing a user-defined function as the
argument and an experiment identifier as an additional ...
argument. The function would have to query the data base for the
plate information using this identifier and return a table as
described above, where the
Filename column contains
identifiers needed to fetch the respective raw data for a single
plate in a subsequent query. Alternatively, this could be a data
base handle, or the query itself.
Providing a second user-defined function as the
importFun argument, which takes the value of the
Filename column for a single plate and retrieves the
respective raw data from the data base.
An object of class
cellHTS, which extends the
After calling this function, the content of the following slots is as follows:
an object of class
information about the runs, inferred from the
the information about the plate and well
identifiers for each plate measurement are stored in columns
a data.frame containing what was read from input file
a list, where each component contains a copy of
the imported input data files. Its length corresponds to the number
of rows of
Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of cell-based RNAi screens, Genome Biology 7, R66.
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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)
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