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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 0f382a5296aae9bfc77df06b0a5ad493eb3c01f3
author ethevenot
date Wed, 28 Feb 2018 10:04:14 -0500
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1 Multivariate analysis by PCA, PLS(-DA), and OPLS(-DA)
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2 =====================================================
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4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure
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6 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/multivariate.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/multivariate).
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8 ### Description
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10 **Version:** 2.3.8
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11 **Date:** 2016-10-21
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12 **Author:** Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)
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13 **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr)
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14 **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)
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15 **Licence:** CeCILL
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16 **Reference history:** [W4M00001a_sacurine-subset-statistics](http://galaxy.workflow4metabolomics.org/history/list_published), [W4M00001b_sacurine_complete](http://galaxy.workflow4metabolomics.org/history/list_published)
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17 **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)
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19 ### Installation
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21 * Configuration file: `multivariate_config.xml`
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22 * Image files:
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23 + `static/images/multivariate_workflowPositionImage.png`
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24 + `static/images/multivariate_workingExampleImage.png`
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25 * Wrapper file: `multivariate_wrapper.R`
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26 * R packages
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27 + **batch** from CRAN
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29 ```r
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30 install.packages("batch", dep=TRUE)
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31 ```
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33 + **ropls** from Bioconductor
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35 ```r
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36 source("http://www.bioconductor.org/biocLite.R")
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37 biocLite("ropls")
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38 ```
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40 ### Tests
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42 The code in the wrapper can be tested by running the `runit/multivariate_runtests.R` R file
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44 You will need to install **RUnit** package in order to make it run:
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45 ```r
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46 install.packages('RUnit', dependencies = TRUE)
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47 ```
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49 ### Working example
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51 See the **W4M00001a_sacurine-subset-statistics**, **W4M00001b_sacurine-subset-complete**, **W4M00002_mtbls2**, **W4M00003_diaplasma** shared histories in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)
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53 ### News
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55 ###### CHANGES IN VERSION 2.3.8
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57 MINOR MODIFICATION
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59 * (O)PLS(-DA) coefficients display in case of multiple quantitative (or multiclass) response: now the column names of the coefficients for each response are correctly labelled in the variableMetadata file
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61 ###### CHANGES IN VERSION 2.3.6
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63 INTERNAL MODIFICATION
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65 * minor internal modifications
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67 ###### CHANGES IN VERSION 2.3.4
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69 INTERNAL MODIFICATION
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71 * minor update of .shed.yml
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73 ###### CHANGES IN VERSION 2.3.2
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75 INTERNAL MODIFICATION
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77 * 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)
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79 ###### CHANGES IN VERSION 2.3.0
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81 NEW FEATURES
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83 * **Predictions** now available (see the 'Samples to be tested' argument)
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84 * OPLS(-DA): **Predictive and Orthogonal VIP** are now computed (see the 'comments' section)
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85 * **Multiclass PLS-DA** implemented (see the 'comments' section)