CobsFitClass-class: Class “CobsFitClass”

Description

The CobsFitClass class represents models that were fit with the nonparametric model.

Usage

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

Value

The fitted method returns a numeric vector.

Arguments

object: object of class CobsFitClass
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

model:: object of class cobs summarizing nonparametric fit
lambda:: numeric

Extends

Class FitClass, directly.

Methods

fitSeries: signature(object = "CobsFitClass"):
Finds the concentration for an individual dilution series given the curve fit for the slide.
fitSlide: signature(object = "CobsFitClass"):
Uses the concentration and intensity series for an entire slide to fit a curve for the slide of intensity = f(conc).
fitted: signature(object = "CobsFitClass"):
Extracts fitted values of the model.
trimConc: signature(object = "CobsFitClass"):
Returns concentration and intensity cutoffs for the model.

Author

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