Mercurial > repos > ethevenot > multivariate
diff README.md @ 0:fafba524dca6 draft
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
author | ethevenot |
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date | Wed, 27 Jul 2016 11:22:56 -0400 |
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children | da272496b32d |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Wed Jul 27 11:22:56 2016 -0400 @@ -0,0 +1,67 @@ +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). + +***