ROC {cellHTS}R Documentation

Creates an object of class "ROC" which can be plotted as a ROC curve

Description

The function ROC construct an object of S3 class ROC, which represents a receiver-operator-characteristic curve, from the data of the annotated positive and negative controls in a scored cellHTS object.

Usage

ROC(x, positives="pos", negatives = "neg")
## S3 method for class 'ROC':
plot(x, col="darkblue", type="l", ...)
## S3 method for class 'ROC':
lines(x, ...)

Arguments

x a cellHTS object that has already been scored (see details).
positives a character string corresponding to the name used to annotate the positive controls in the cellHTS object.
negatives a character string corresponding to the name used to annotate the negative controls in the cellHTS object.
col the graphical parameter for color; see par for details.
type the graphical parameter giving the type of plot desired; see par for details.
... other graphical parameters as in par may be also passed as arguments.

Details

The cellHTS object x must contain a slot called score, and selection proceeds from large to small values of this score. Furthermore, x is expected to contain positive and negative controls annotated in the slot wellAnno with the values of the arguments positives and negatives, respectively.

Value

An S3 object of class ROC. There are methods plot.ROC and lines.ROC.

Author(s)

W. Huber huber@ebi.ac.uk

Examples

 datadir = system.file("KcViabSmall", package = "cellHTS")
 x = readPlateData("Platelist.txt", "KcViabilitySmall", 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)
 x = normalizePlateMedian(x, zscore="-")
 x = summarizeReplicates(x)
 y = ROC(x)
 plot(y)
 lines(y)

[Package cellHTS version 1.2.0 Index]