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, plateType="384", verbose=TRUE)
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. |
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.
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. |
W. Huber huber@ebi.ac.uk
..
datadir = system.file("KcViabSmall", package = "cellHTS") x = readPlateData("Platelist.txt", "KcViabSmall", path=datadir)