R: Class "CobsFitClass"

CobsFitClass-class {RPPASPACE}

R Documentation

Class “CobsFitClass”

Description

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

Usage

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

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

Value

The fitted method returns a numeric vector.

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(s)

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