configure {cellHTS2} | R Documentation |
Annotate the plates and the plate result files of a cellHTS
object.
## S4 method for signature 'cellHTS': configure(object, descripFile, confFile, logFile, path)
object |
a cellHTS object. |
descripFile |
the name of the screen description file (see details).
This argument is just passed on to the readLines
function, so any of the valid argument
types for readLines are valid here, too. |
confFile |
the name of the configuration file (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.
Must contain one row for each well and each batch. |
logFile |
optional; the name of the screen log file (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 |
optional; a character of length one indicating the path in which to find the configuration files. It can be useful when the files are located in the same directory, and may be omitted otherwise. |
The configuration has three components:
confFile: This file specifies where the controls are. This file
is expected to be a tab-delimited file with two first header rows giving
the total number of wells and plates in the screen. The next rows should
be in the form of a spreadsheet table with at least three columns named
Plate
, Well
and Content
. Columns Plate
and
Well
are allowed to contain regular expressions. Data from wells
that are configured as empty will be ignored and are set to
NA
in the data slot xraw
. For an example, and for more
details, please read the accompanying vignette.
logFile: This optional file allows to flag certain measurements
as invalid. It is expected to be a tab-delimited file with at least
three columns, and column names Plate
, Well
, and
Flag
. If there are multiple samples (replicates or conditions), a
column called Sample
should also be given. If there are multiple channels, a column called
Channel
must be given. Further columns are allowed.
descripFile: The screen description file contains general information about the screen.
An S4 object of class cellHTS
,
which is obtained by copying object
and updating
the following slots:
plateConf |
a data frame containing what was read from input file confFile (except the first two header rows). |
screenLog |
a data frame containing what was read from input file logFile . |
screenDesc |
object of class character containing what was read from input file descripFile . |
state |
the processing status of the cellHTS object is updated in to state["configured"]=TRUE . |
featureData |
the column controlStatus is updated taking into account the well annotation given by the plate configuration file. |
experimentData |
an object of class MIAME containing descriptions of the
experiment, constructed from the screen description file. |
Wolfgang 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.
readPlateList
templateDescriptionFile
datadir <- system.file("KcViabSmall", package = "cellHTS2") x <- readPlateList("Platelist.txt", name="KcViabSmall", path=datadir) x <- configure(x, "Description.txt", "Plateconf.txt", "Screenlog.txt", path=datadir)