Class DiStatis DiStatis S4 class (kimod: k-tables approach to integrate multiple Omics-Data Multiple dataset)

Description

Statis with Distance options implementation.

Features

1. DiStatis (Statis with Distance options)

2. Bootstrap Implementation

3. Biplot Implementation with variable selection

4. Clustering of variables

5. Plotting compromise, bootstrap, trajectories, Biplot.

Fields

• distances.methods: The character indicating the metrics used.

• Inertia.RV: Inertia (%) explained for all tables.

• RV: Vectorial Correlation Matrix between studies.

• Euclid.Im: Euclidean Image of all studies.

• Inertia.Comp: Inertia (%) explained for all dimensions of compromise matrix.

• Compromise.Coords: Projection of all observations in compromise (Coords).

• Compromise.Matrix: Compromise Matrix from statis methodology.

• RQO: Representation Quality of observations in compromise matrix.

• Trajectories: List of trajectories from Statis methodology

Accesors

• Inertia.RV(x), Inertia.RV(x) <- value: Inertia (%) explained for all tables.

• RV(x), RV(x) <- value: Vectorial Correlation Matrix between studies.

• Euclid.Im(x),Euclid.Im(x) <- value : Euclidean Image of all studies.

• Inertia.Comp(x),Inertia.Comp(x) <- value :: Inertia (%) explained for all dimensions of compromise matrix.

• Compromise.Coords(x),Compromise.Coords(x) <- value: Projection of all observations in compromise (Coords).

• Compromise.Matrix(x),Compromise.Matrix(x) <- value: Compromise Matrix from statis methodology.

• RQO(x),RQO(x) <- value: Representation Quality of observations in compromise matrix.

• Trajectories(x),Trajectories(x) <- value: List of trajectories from Statis methodology.

DiStatis-general-functions

print

Basic output for DiStatis class

summary

Basic statistics for DiStatis class

DiStatis

Getters for their respective slots.

Author(s)

M L Zingaretti, J A Demey-Zambrano, J L Vicente Villardon, J R Demey

References

1. Abdi, H., Williams, L.J., Valentin, D., & Bennani-Dosse, M. (2012). STATIS and DISTATIS: optimum multitable principal component analysis and three way metric multidimensional scaling. WIREs Comput Stat, 4, 124-167.

2. Escoufier, Y. (1976). Operateur associe a un tableau de donnees. Annales de laInsee, 22-23, 165-178.

3. Escoufier, Y. (1987). The duality diagram: a means for better practical applications. En P. Legendre & L. Legendre (Eds.), Developments in Numerical Ecology, pp. 139-156, NATO Advanced Institute, Serie G. Berlin: Springer.

4. L'Hermier des Plantes, H. (1976). Structuration des Tableaux a Trois Indices de la Statistique. [These de Troisieme Cycle]. University of Montpellier, France.

See Also

CompPlot, Biplot DiStatis, and additional related DiStatis class functions.

Examples

 showClass("DiStatis")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(kimod)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/kimod/DiStatis-Class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: DiStatis-class
> ### Title: Class 'DiStatis' DiStatis S4 class (kimod: k-tables approach to
> ###   integrate multiple Omics-Data Multiple dataset)
> ### Aliases: class:DiStatis DiStatis-class DiStatis-class Inertia.RV
> ###   Inertia.RV,DiStatis-method Inertia.RV<-,DiStatis-method RV
> ###   RV,DiStatis-method RV<-,DiStatis-method Euclid.Im
> ###   Euclid.Im,DiStatis-method Euclid.Im<-,DiStatis-method Inertia.comp
> ###   Inertia.comp,DiStatis-method Inertia.comp<-,DiStatis-method
> ###   Compromise.Coords Compromise.Coords,DiStatis-method
> ###   Compromise.Coords<-,DiStatis-method Compromise.Matrix
> ###   Compromise.Matrix,DiStatis-method Compromise.Matrix<-,DiStatis-method
> ###   RQO RQO,DiStatis-method RQO<-,DiStatis-method Trajectories
> ###   Trajectories,DiStatis-method Trajectories<-,DiStatis-method
> 
> ### ** Examples
> 
>  showClass("DiStatis")
Class "DiStatis" [package "kimod"]

Slots:
                                                                              
Name:  distances.methods        Inertia.RV                RV         Euclid.Im
Class:         character        data.frame            matrix        data.frame
                                                                              
Name:       Inertia.comp Compromise.Coords Compromise.Matrix               RQO
Class:            matrix        data.frame        data.frame            matrix
                                                                              
Name:       Trajectories            RowMar            ColMar              Data
Class:              list            matrix        data.frame              list
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>