readPlateData {cellHTS} | 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 x
.
readPlateData(filename, path=dirname(filename), name, importFun, verbose=TRUE, plateType)
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 . |
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. |
plateType |
(deprecated argument) a character of length 1 giving the format of the plate: "96" for 96-well plate format, or "384" for a 384-well plate format. |
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
, 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
.
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, containing the imported measurement data. |
pdim |
a numeric vector of length 2 containing the number of rows
and columns in a plate. The product of these two numbers is the
first dimension of xraw . This corresponds to the plate
format used in the screen, and it is automatically determined from the plate result files. The allowed formats are 96-well or 384-well plates.
|
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, where each component contains 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. |
W. Huber huber@ebi.ac.uk, Ligia Braz ligia@ebi.ac.uk
datadir <- system.file("KcViabSmall", package = "cellHTS") x <- readPlateData("Platelist.txt", "KcViabSmall", path=datadir) ## To read data files obtained from an EnVision plate reader: datadir <- system.file("EnVisionExample", package = "cellHTS") x <- readPlateData("platelist.txt", "EnVisionEx", importFun=getEnVisionRawData, path=datadir) ## to get the cross talk corrected data: y <- readPlateData("platelist.txt", "EnVisionEx", importFun=getEnVisionCrosstalkCorrectedData, path=datadir)