annotate README.md @ 1:da272496b32d draft

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author ethevenot
date Sat, 30 Jul 2016 12:31:20 -0400
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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) project
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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:** 2.3.4
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11 **Date:** 2016-07-30
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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 `tests/multivariate_tests.R` in R.
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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 ## News
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51 ### CHANGES IN VERSION 2.3.4
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53 INTERNAL MODIFICATION
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55 * minor update of .shed.yml
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57 ***
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59 ### CHANGES IN VERSION 2.3.2
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61 INTERNAL MODIFICATION
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63 * 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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65 ***
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67 ### CHANGES IN VERSION 2.3.0
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69 NEW FEATURES
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71 * **Predictions** now available (see the 'Samples to be tested' argument).
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72 * OPLS(-DA): **Predictive and Orthogonal VIP** are now computed (see the 'comments' section).
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73 * **Multiclass PLS-DA** implemented (see the 'comments' section).
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75 ***