cellHTS
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).
readPlateList(filename, path=NA, name="anonymous", importFun,
dec=".", verbose=interactive(), ...)read.table function,
so any of the valid argument types for the file argument of
read.table are valid here, too. Alternatively, a
user-defined function which is supposed to create a table-like R
object of the plate list. Additional arguments to
readPlateList in ... will be passed on to this function.importFun argument is
supplied, the value of path will not be automatically
prepended to the file names. This has to be explicitely dealt with
in the importFun function. See details.. to represent the decimal point (e.g., the comma ,).filename if it is a function.cellHTS, which extends the
class NChannelSet.After calling this function, the content of the following slots is as
follows: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.plateList file: which replicate, which variant of the assay,
treatment, incubation times etc.plate and well of this slot.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.plateList. The plate list 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. Filename should
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
base queries.
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:
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.
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.
Direct data base import without the need for any flat files at all could for instance be achieved by:
filename
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.
importFun argument, which takes the value of the
Filename column for a single plate and retrieves the
respective raw data from the data base.
readHTAnalystData. To build a cellHTS2 object from a
data frame, see buildCellHTS2.
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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