Mercurial > repos > ethevenot > multivariate
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author | ethevenot |
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date | Sat, 30 Jul 2016 12:31:20 -0400 |
parents | fafba524dca6 |
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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:** 2.3.4 **Date:** 2016-07-30 **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 **Reference history:** [W4M00001a_sacurine-subset-statistics](http://galaxy.workflow4metabolomics.org/history/list_published), [W4M00001b_sacurine_complete](http://galaxy.workflow4metabolomics.org/history/list_published) **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 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 2.3.4 INTERNAL MODIFICATION * minor update of .shed.yml *** ### 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). ***