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1 # Univariate parametric and non-parametric hypothesis testing with correction for multiple testing 1 Univariate parametric and non-parametric hypothesis testing with correction for multiple testing
2 ================================================================================================
2 3
3 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project. 4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure
4 5
5 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/univariate.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/univariate). 6 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/univariate.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/univariate).
6 7
7 ## Description 8 ### Description
8 9
9 **Version:** 2.1.2 10 **Version:** 2.1.4
10 **Date:** 2016-07-30 11 **Date:** 2016-08-05
11 **Author:** Marie Tremblay-Franco (INRA, MetaToul, MetaboHUB, W4M Core Development Team) and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team) 12 **Author:** Marie Tremblay-Franco (INRA, MetaToul, MetaboHUB, W4M Core Development Team) and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)
12 **Email:** [marie.tremblay-franco(at)toulouse.inra.fr](mailto:marie.tremblay-franco@toulouse.inra.fr); [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) 13 **Email:** [marie.tremblay-franco(at)toulouse.inra.fr](mailto:marie.tremblay-franco@toulouse.inra.fr); [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr)
13 **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) 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)
14 **Reference history:** [W4M00001a_sacurine-subset-statistics](http://galaxy.workflow4metabolomics.org/history/list_published), [W4M00004_mtbls1](http://galaxy.workflow4metabolomics.org/history/list_published) 15 **Reference history:** [W4M00001a_sacurine-subset-statistics](http://galaxy.workflow4metabolomics.org/history/list_published), [W4M00004_mtbls1](http://galaxy.workflow4metabolomics.org/history/list_published)
15 **Licence:** CeCILL 16 **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 **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
18 ## Installation 19 ### Installation
19 20
20 * Configuration file: **univariate_config.xml** 21 * Configuration file: `univariate_config.xml`
21 * Image file: 22 * Image file:
22 + **static/images/univariate_workflowPositionImage.png** 23 + `static/images/univariate_workflowPositionImage.png`
23 * Wrapper file: **univariate_wrapper.R** 24 * Wrapper file: `univariate_wrapper.R`
24 * Script file: **univariate_script.R** 25 * Script file: `univariate_script.R`
25 * R packages 26 * R packages
26 + **batch** from CRAN: `install.packages("batch", dep=TRUE)`. 27 + **batch** from CRAN
27 + **PMCMR** from Bioconductor: `install.packages("PMCMR", dep=TRUE)`. 28
29 ```r
30 install.packages("batch", dep=TRUE)
31 ```
32 + **PMCMR** from CRAN
33
34 ```r
35 install.packages("PMCMR", dep=TRUE)
36 ```
37
38 ### Tests
28 39
29 ## Tests 40 The code in the wrapper can be tested by running the `runit/univariate_runtests.R` R file
30 41
31 The code in the wrapper can be tested by running the **tests/univariate_tests.R** in R 42 You will need to install **RUnit** package in order to make it run:
43 ```r
44 install.packages('RUnit', dependencies = TRUE)
45 ```
32 46
33 ## News 47 ### Working example
34 48
35 ## CHANGES IN VERSION 2.1.2 49 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)
50
51 ### News
52
53 ###### CHANGES IN VERSION 2.1.4
54
55 NEW FEATURE
56
57 Level names are now separated by '.' instead of '-' previously in the column names of the output variableMetadata table (e.g., 'jour_ttest_J3.J10_fdr' instead of 'jour_ttest_J3-J10_fdr' previously)
58
59 INTERNAL MODIFICATION
60
61 * Minor internal changes
62
63 ###### CHANGES IN VERSION 2.1.2
64
65 INTERNAL MODIFICATION
36 66
37 * Minor internal changes in .shed.yml for toolshed export 67 * Minor internal changes in .shed.yml for toolshed export
38 68
39 ## CHANGES IN VERSION 2.1.1 69 ###### CHANGES IN VERSION 2.1.1
70
71 INTERNAL MODIFICATION
40 72
41 * Internal handling of 'NA' p-values (e.g. when intensities are identical in all samples). 73 * Internal handling of 'NA' p-values (e.g. when intensities are identical in all samples).