LogisticFitClass-class: Class “LogisticFitClass”

Description

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

Usage

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

Value

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

The fitted method returns a numeric vector.

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 EC50 dilution
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 RPPADesignParams describing options for processing the array
trimLevel: numeric scalar multiplied to Median Absolute Deviation MAD
...: extra arguments for generic routines

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

P. Roebuck paul_roebuck@comcast.net, James M. Melott jmmelott@mdanderson.org