---
title: "Real Datasets Application"
lang: "en"
output:
  rmarkdown::html_vignette:
    css: vignette.css
vignette: >
  %\VignetteIndexEntry{Real Datasets Application}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---
```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#"
  )

```

<style>
/*body {background-color: powderblue;}*/
h1   {color: blue;}
p    {color: black;}
</style>


<div class="top"><a class="toplink" href="#nav" title="&uArr; top">&nbsp;</a></div>
<div id="nav">
<ul>
<li>[vignetteMult](vignetteMult.html "MultiGroupO vignette")</li>
<li>[datR](datR.html "Real Datasets Application")</li>
</ul>
</div>


# Description 
Gene expression data from Khan et al. (2001).
This data set contains 83 samples with 2308 genes: 29 cases of Ewing sarcoma (EWS), 
coded 1, 11 cases of Burkitt lymphoma (BL), coded 2, 18 cases of neuroblastoma (NB), 
coded 3, 25 cases of rhabdomyosarcoma (RMS), coded 4. A total of 63 training samples 
and 25 test samples are provided in Khan et al. (2001). Five of the test set are 
non-SRBCT and are not considered here. 
The training sample indexes correspond to 1:65 and the test sample indexes 
(without non-SRBCT sample) correspond to 66:83.


# Standard PCA method
```{r setup}
library(plsgenomics)
library(MultiGroupO)
data(SRBCT)
 mydata<-SRBCT$X
 mydata<-mydata[,1:5]
 groups<-as.factor(SRBCT$Y)
 pca(datos=mydata,grupos=groups,Plot=TRUE,center=TRUE,scale=TRUE)
      
```
# Multigroup PCA method
```{r setup1}
library(plsgenomics)
data(SRBCT)
mydata<-SRBCT$X
mydata<-mydata[,1:5]
groups<-as.factor(SRBCT$Y)
mat.to.diag1<-new.cov(x=mydata,cls=groups,A=diag(ncol(mydata)))
mgpca(mat.to.diag=mat.to.diag1,mat.x=as.matrix(mydata),cls=groups,Plot=TRUE,ncomp=2,center = TRUE,scale = TRUE)
```

# MDR method
```{r setup2}
library(plsgenomics)
data(SRBCT)
mydata<-SRBCT$X
mydata<-mydata[,1:5]
groups<-as.factor(SRBCT$Y)
mydata<-split(as.data.frame(mydata),groups)
mdr(group=groups,data.x=mydata,c=2)
