This function calculates the biplot method through the compromise matrix to select genes
SelectVar from DiStatis Class Object
High level constructor of SelectVar class object
Usage
SelectVar(object, ord = FALSE, Crit = c("R2-Adj", "p-val(Bonf)", "AIC",
"BIC"), perc = 0.9, Dims = 2)
## S4 method for signature 'DiStatis'
SelectVar(object, ord = FALSE, Crit = c("R2-Adj",
"p-val(Bonf)", "AIC", "BIC"), perc = 0.9, Dims = 2)
Arguments
object
Object is an object of DiStatis Class.
ord
Logical. If TRUE, the models with intercept are computed, else the intercept is zero.
Crit
c("R2-Adj","p-val(Bonf)","AIC","BIC").Criterious of selection. "R2-Adj","p-val (Bonf)","AIC","BIC". Choose "R2-Adj" or "p-val (Bonf)" (Bonferroni correction),"AIC" or "BIC".
perc
The value of percentil that indicate how much data than are selected.
Dims
Numeric that indicates the number of dimensions to use for do the model. Default is 2.
Details
This function allows to build the biplot for continuous response, using an external procedure
to obtained the regresors in the linear model (the response being an continuous variable).
This function allows the selection of genes using the goodness of fit of the Models Biplot.
object,ord=FALSE,
Value
SelectVar
SelectVar class object with the
corresponding completed slots
according to the given model
Author(s)
M L Zingaretti, J A Demey-Zambrano, J L Vicente Villardon, J R Demey
References
Demey, J., Vicente-Villardon, J. L., Galindo, M.P. & Zambrano, A. (2008) Identifying Molecular Markers Associated With Classification Of Genotypes Using External Logistic Biplots. Bioinformatics, 24(24), 2832-2838.
Gabriel, K. (1971). The biplot graphic display of matrices with application to principal component analysis. Biometrika 58(3), 453–467.
Gower, J. & Hand, D. (1996). Biplots, Monographs on statistics and applied probability. 54. London: Chapman and Hall., 277 pp.
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-SelectVar.Rd_%03d_medium.png", width=480, height=480)
> ### Name: SelectVar
> ### Title: Function 'SelectVar' of DiStatis object
> ### Aliases: SelectVar SelectVar,DiStatis-method SelectVar-methods
>
> ### ** Examples
>
> {
+ data(NCI60Selec)
+ Z1<-DiStatis(NCI60Selec)
+ M1<-SelectVar(Z1,Crit="R2-Adj",perc=0.95)
+ M2<-SelectVar(Z1,Crit="p-val(Bonf)",perc=0.95)
+ }
The calculations were performed using the scalar product between the tables
The Projection of all variables will be made when the number of variables is less than 50
>
>
>
>
>
>
> dev.off()
null device
1
>