readPlateList {cellHTS2} | R Documentation |
Reads a collection of plate reader data files into a cellHTS
object.
The names of the files, plus additional information
(plate number, repeat number, assay/treatment/condition)
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. |
name |
a character of length 1 with the experiment name. |
importFun |
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, the import function needs to be adapted. See details. |
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 named Filename
, Plate
,
and Replicate
. The contents of the columns Plate
and
Replicate
are expected to be integers. Further columns are
allowed, and can be used to denote, for example, different variants of the
assay, treatments, incubation times, conditions, etc.
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 file table (which in
principle do not need to be individual files, they could also be handles for
database entries or pointers into relevants parts of a file). 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
.
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 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. |
phenoData |
information about the runs, infered from the
plateList file: which replicate, which variant of the
assay, treatment, incubation times etc. |
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)