Class “CobsFitClass”

Description

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

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
## 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 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 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 proebuck@mdanderson.org

References

Hu J, He X, Baggerly KA, Coombes KR, Hennessy BT, Mills GB.
"Non-parametric Quantification of Protein Lysate Arrays"
Bioinformatics (2007) 23(15): 1986-1994.
http://bioinformatics.oxfordjournals.org/content/23/15/1986

See Also

FitClass

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.