configure {cellHTS} | R Documentation |
Annotate the plates and the plate result files of a given cellHTS object.
configure(x, ...) ## S3 method for class 'cellHTS': configure(x, confFile, logFile, descripFile, ...)
x |
a cellHTS object. |
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 |
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. |
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. |
... |
additional parameters - ignored. |
Batch
, Position
,
Well
and Content
. The contents of Position
are expected
to be integer.Filename
, Well
,
and Flag
. Further columns are allowed.
Data from wells that are annotated as empty are ignored and are set to NA in x
in slot xraw
.
An S3 object of class cellHTS
, which extends the argument x
by the following elements:
plateConf |
a data.frame containing what was read from input file confFile . The number of rows is equal to the product between the number of wells in each plate and the number of batches. |
screenLog |
a data.frame containing what was read from input file logFile . |
wellAnno |
object of class factor of length number of plates x number of wells per plate, with five possible levels: empty, other, neg, sample, and pos, indicative of the contents of the wells. |
screenDesc |
object of class character containing what was read from input file descripFile . |
Moreover, the processing status of the cellHTS
object is updated in the slot state
to state["configured"]=TRUE
.
There are methods print.cellHTS
, configure.cellHTS
and annotate.cellHTS
.
Wolfgang Huber huber@ebi.ac.uk, Ligia Braz ligia@ebi.ac.uk
..
datadir = system.file("KcViabSmall", package = "cellHTS") x = readPlateData("Platelist.txt", "KcViabSmall", path=datadir) confFile = system.file("KcViabSmall", "Plateconf.txt", package="cellHTS") logFile = system.file("KcViabSmall", "Screenlog.txt", package="cellHTS") descripFile = system.file("KcViabSmall", "DESCRIPTION.txt", package="cellHTS") x = configure(x, confFile, logFile, descripFile)