Mercurial > repos > ethevenot > multivariate
comparison 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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1 Multivariate analysis by PCA, PLS(-DA), and OPLS(-DA) | |
2 ===================================================== | |
3 | |
4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project | |
5 | |
6 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/multivariate.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/multivariate). | |
7 | |
8 ## Description | |
9 | |
10 **Version:** 2.3.2 | |
11 **Date:** 2016-05-15 | |
12 **Author:** Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team) | |
13 **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) | |
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) | |
15 **Licence:** CeCILL | |
16 **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) | |
17 | |
18 ## Installation | |
19 | |
20 * Configuration file: `multivariate_config.xml`. | |
21 * Image files: | |
22 + `static/images/multivariate_workflowPositionImage.png`. | |
23 + `static/images/multivariate_workingExampleImage.png`. | |
24 * Wrapper file: `multivariate_wrapper.R`. | |
25 * R packages | |
26 + **batch** from CRAN | |
27 | |
28 ```r | |
29 install.packages("batch", dep=TRUE) | |
30 ``` | |
31 | |
32 + **ropls** from Bioconductor | |
33 | |
34 ```r | |
35 install.packages("batch", dep=TRUE) | |
36 source("http://www.bioconductor.org/biocLite.R") | |
37 biocLite("ropls") | |
38 ``` | |
39 | |
40 ## Tests | |
41 | |
42 The code in the wrapper can be tested by running the `tests/multivariate_tests.R` in R. | |
43 | |
44 You will need to install **RUnit** package in order to make it run: | |
45 ```r | |
46 install.packages('RUnit', dependencies = TRUE) | |
47 ``` | |
48 | |
49 ## News | |
50 | |
51 ### CHANGES IN VERSION 2.3.2 | |
52 | |
53 INTERNAL MODIFICATION | |
54 | |
55 * 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). | |
56 | |
57 *** | |
58 | |
59 ### CHANGES IN VERSION 2.3.0 | |
60 | |
61 NEW FEATURES | |
62 | |
63 * **Predictions** now available (see the 'Samples to be tested' argument). | |
64 * OPLS(-DA): **Predictive and Orthogonal VIP** are now computed (see the 'comments' section). | |
65 * **Multiclass PLS-DA** implemented (see the 'comments' section). | |
66 | |
67 *** |