sc21-RPPAPreFitQC-class: Class "RPPAPreFitQC"

In SuperCurve: RPPA Analysis Package

Description

The RPPAPreFitQC class represents the inputs necessary to determine the quality control rating of a reverse-phase protein array slide.

Usage

RPPAPreFitQC(rppa, design, useAdjusted=FALSE)
is.RPPAPreFitQC(x)
## S4 method for signature 'RPPAPreFitQC'
qcprob(object, ...)
## S4 method for signature 'RPPAPreFitQC'
summary(object, ...)

Arguments

rppa	object of class RPPA containing the raw data to be assessed
design	object of class RPPADesign describing the layout of the array
useAdjusted	logical scalar. If TRUE, spatially adjusted measures are used instead of Mean.Net and Mean.Total.
object	object of (sub)class RPPAPreFitQC
x	object of (sub)class RPPAPreFitQC
...	extra arguments for generic routines

Value

The RPPAPreFitQC generator returns an object of subclass of class RPPAPreFitQC.

The is.RPPAPreFitQC method returns TRUE if its argument is an object of subclass of class RPPAPreFitQC.

The summary method returns a summary of the underlying data frame.

Objects from the Class

Objects are created by calls to the RPPAPreFitQC factory method.

Methods

qcprob

signature(object = "RPPAPreFitQC"):
Placeholder method which must be implemented by subclass.

summary

signature(object = "RPPAPreFitQC"):
Placeholder method which must be implemented by subclass.

Warning

The current implementation only handles designs with 5 dilution series.
Anything else will fail.

Author(s)

P. Roebuck [e-mail]

Examples

extdata.dir <- system.file("extdata", package="SuperCurveSampleData")

txtdir <- file.path(extdata.dir, "rppaSingleSubgridData")
rppa <- RPPA("Foo.txt",
             path=txtdir,
             software="microvigene",
             alt.layout="superslide")
designfile <- file.path(txtdir, "slidedesign.tsv")
design <- RPPADesign(rppa, designfile=designfile)
fitqc <- RPPAPreFitQC(rppa, design)
summary(fitqc)
qcprob(fitqc)

SuperCurve documentation built on May 2, 2019, 6:14 p.m.