Class "MixModel"

Description

This class stores a fitted mixture model.

Objects from the Class

A virtual Class: No objects may be created from it.

Slots

mmData:

Object of class "numeric" storing the data.

configuration:

Object of class "list" storing configuration. See notes for details.

results:

Object of class "list" storing results. See notes for details.

Methods

as.data.frame

signature(object = "MixModel"): Returns a data.frame containing the z-scores and classification results. The optional argument classificationMethod can be used to change the default classification method.

classification

signature(object = "MixModel", method = "character"): Assess classification results.

classification

signature(object = "MixModel", method = "missing"): Assess classification results.

components

signature(object = "MixModel"): Assess mixture components.

mmData

signature(object = "MixModel"): Assess data.

dim

signature(x = "MixModel"): Assess dimension, i.e. numer of data points and number of components.

length

signature(x = "MixModel"): Number of data points.

listClassificationMethods

signature(object = "MixModel"): List available classification methods.

show

signature(object = "MixModel"): Print an object of MixModel on screen.

summary

signature(object = "MixModel"): Returns a list of data frames summarizing the parameter estimations for each component.

weights

signature(object = "MixModel"): Asses the components weights.

Note

Slots configuration and results are lists with named elements. The following elements make up the minimum set of element that must be present. Depending on the method that was used to fit the mixture model, more elements may be present.

Slot configuration has at least one element.

1. inits A list with at least two elements: component and pi. components contains a list of objects of MixtureComponent-class storing the inital parameters of the mixture components. pi is a vector storing the initial components' weights.

Slot results has at least three elements.

1. components A list of objects of MixtureComponent-class storing the fitted mixture components.

2. pi A numeric vector holding the estimated components' weights.

3. classification A list of numeric vectors of the same length as data storing the classification results.

Author(s)

Hans-Ulrich Klein (h.klein@uni-muenster.de)

See Also

mlMixModel bayesMixModel MixModelML MixModelBayes

Examples

showClass("MixModel")

Results

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> library(epigenomix)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/epigenomix/MixModel-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MixModel-class
> ### Title: Class '"MixModel"'
> ### Aliases: MixModel-class as.data.frame,MixModel-method classification
> ###   classification,MixModel,character-method
> ###   classification,MixModel,missing-method components
> ###   components,MixModel-method mmData mmData,MixModel-method
> ###   dim,MixModel-method length,MixModel-method listClassificationMethods
> ###   listClassificationMethods,MixModel-method show,MixModel-method
> ###   summary,MixModel-method summary,MixModelBayes-method
> ###   weights,MixModel-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("MixModel")
Virtual Class "MixModel" [package "epigenomix"]

Slots:
                                                
Name:         mmData configuration       results
Class:       numeric          list          list

Known Subclasses: "MixModelBayes", "MixModelML"
> 
> 
> 
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> 
> dev.off()
null device 
          1 
>