sc08-LogisticFitClass-class: Class "LogisticFitClass"

In SuperCurve: RPPA Analysis Package

Description

The LogisticFitClass class represents models that were fit with the logistic model.

Usage

## S4 method for signature 'LogisticFitClass'
coef(object, ...)
## S4 method for signature 'LogisticFitClass'
coefficients(object, ...)
## S4 method for signature 'LogisticFitClass'
fitSeries(object,
          diln,
          intensity,
          est.conc,
          method="nls",
          silent=TRUE,
          trace=FALSE,
          ...)
## S4 method for signature 'LogisticFitClass'
fitSlide(object,
         conc,
         intensity,
         ...)
## S4 method for signature 'LogisticFitClass'
fitted(object,
       conc,
       ...)
## S4 method for signature 'LogisticFitClass'
trimConc(object,
         conc,
         intensity,
         design,
         trimLevel,
         ...)

Arguments

object	object of class LogisticFitClass
diln	numeric vector of dilutions for series to be fit
intensity	numeric vector of observed intensities for series to be fit
est.conc	numeric estimated concentration for dilution = 0
method	character string specifying regression method to use to fit the series
silent	logical scalar. If TRUE, report of error messages will be suppressed in try(nlsmeth(...))
trace	logical scalar. Used in nls method.
conc	numeric vector containing estimates of the log concentration for each dilution series
design	object of class RPPADesign describing the layout of the array
trimLevel	numeric scalar multiplied to MAD
...	extra arguments for generic routines

Value

The coef and coefficients methods return a named vector of length three with logistic curve coefficients.

The fitted method returns a numeric vector.

Objects from the Class

Objects are created internally by calls to the methods fitSlide or RPPAFit.

Slots

coefficients:

numeric vector of length 3, representing alpha, beta, and gamma respectively.

Extends

Class FitClass, directly.

Methods

coef

signature(object = "LogisticFitClass"):
Extracts model coefficients from objects returned by modeling functions.

coefficients

signature(object = "LogisticFitClass"):
An alias for coef

fitSeries

signature(object = "LogisticFitClass"):
Finds the concentration for an individual dilution series given the curve fit for the slide.

fitSlide

signature(object = "LogisticFitClass"):
Uses the concentration and intensity series for an entire slide to fit a curve for the slide of intensity = f(conc).

fitted

signature(object = "LogisticFitClass"):
Extracts fitted values of the model.

trimConc

signature(object = "LogisticFitClass"):
Returns concentration and intensity cutoffs for the model.

Author(s)

P. Roebuck [e-mail]

See Also

FitClass

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