Mercurial > repos > ethevenot > multivariate

Multivariate analysis by PCA, PLS(-DA), and OPLS(-DA)
=====================================================

A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project

Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/multivariate.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/multivariate).

## Description

**Version:** 2.3.2
**Date:** 2016-05-15
**Author:** Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)
**Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr)
**Citation:** Thevenot E.A., Roux A., Xu Y., Ezan E. and Junot C. (2015). Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses. *Journal of Proteome Research*, **14**:3322-3335. [doi:10.1021/acs.jproteome.5b00354](http://dx.doi.org/10.1021/acs.jproteome.5b00354)
**Licence:** CeCILL
**Funding:** Agence Nationale de la Recherche ([MetaboHUB](http://www.metabohub.fr/index.php?lang=en&Itemid=473) national infrastructure for metabolomics and fluxomics, ANR-11-INBS-0010 grant)

## Installation

* Configuration file: `multivariate_config.xml`.
* Image files:
  + `static/images/multivariate_workflowPositionImage.png`.
  + `static/images/multivariate_workingExampleImage.png`.
* Wrapper file: `multivariate_wrapper.R`.
* R packages
  + **batch** from CRAN

    ```r
    install.packages("batch", dep=TRUE)
    ```

  + **ropls** from Bioconductor

    ```r
    install.packages("batch", dep=TRUE)
    source("http://www.bioconductor.org/biocLite.R")
    biocLite("ropls")
    ```

## Tests

The code in the wrapper can be tested by running the `tests/multivariate_tests.R` in R.

You will need to install **RUnit** package in order to make it run:
```r
install.packages('RUnit', dependencies = TRUE)
```

## News

### CHANGES IN VERSION 2.3.2

INTERNAL MODIFICATION

 * Modification of the `multivariate_wrapper.R` file to handle **ropls** package versions of 1.3.15 and above (i.e. after switching to S4 classes).

***

### CHANGES IN VERSION 2.3.0

NEW FEATURES

 * **Predictions** now available (see the 'Samples to be tested' argument).
 * OPLS(-DA): **Predictive and Orthogonal VIP** are now computed (see the 'comments' section).
 * **Multiclass PLS-DA** implemented (see the 'comments' section).

***
author	ethevenot
date	Wed, 27 Jul 2016 11:22:56 -0400
parents
children	da272496b32d