configure {cellHTS2} | R Documentation |
Annotate the plates and the plate result files of a given 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. Useful when the files are locate in the same directory, but should be omitted otherwise. |
Plate
, Well
and Content
. Columns Plate
and Well
are allowed to contain regular expressions.
For more details about the plate configuration file, read the accompanying vignette.
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.
Data from wells that are annotated as empty are ignored and are set to NA in object
in slot xraw
.
An S4 object of class cellHTS
, which extends the class NChannelSet
. The followings slots of object
are updated:
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 having 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.
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)