Migration: univariate

tools/univariate/.gitignore

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+.Rproj.user

tools/univariate/.shed.yml

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+name: univariate
+owner: ethevenot
+description: '[W4M][Metabolomics][LC-MS][GC-MS][NMR] Univariate statistics.'
+homepage_url: http://workflow4metabolomics.org
+long_description: 'The module performs two sample tests (t-test and Wilcoxon rank test), analysis of variance and Kruskal-Wallis rank test, and correlation tests (by using either the pearson or the spearman correlation).'
+remote_repository_url: https://github.com/workflow4metabolomics/tools-metabolomics/
+homepage_url: https://github.com/odisce/
+categories:
+- Metabolomics
+- Transcriptomics
+- Proteomics
+- Statistics

tools/univariate/README.md

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+Univariate parametric and non-parametric hypothesis testing with correction for multiple testing  
+================================================================================================  
+
+A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure    
+
+Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/univariate.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/univariate).
+
+### Description
+
+**Version:** 2.2.4   
+**Date:** 2018-01-11  
+**Author:** Marie Tremblay-Franco (INRA, MetaToul, MetaboHUB, W4M Core Development Team) and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)    
+**Email:** [marie.tremblay-franco(at)toulouse.inra.fr](mailto:[email protected]); [etienne.thevenot(at)cea.fr](mailto:[email protected])  
+**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)  
+**Reference history:** [W4M00001a_sacurine-subset-statistics](http://galaxy.workflow4metabolomics.org/history/list_published), [W4M00004_mtbls1](http://galaxy.workflow4metabolomics.org/history/list_published)  
+**Licence:** CeCILL  
+**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: `univariate_config.xml`  
+ * Image file: 
+  + `static/images/univariate_workflowPositionImage.png`   
+ * Wrapper file: `univariate_wrapper.R`  
+ * Script file: `univariate_script.R`  
+ * R packages  
+  + **batch** from CRAN  
+
+    ```r
+    install.packages("batch", dep=TRUE)  
+    ```
+  + **PMCMR** from CRAN  
+
+    ```r  
+    install.packages("PMCMR", dep=TRUE)  
+    ```    
+
+### Tests
+
+The code in the wrapper can be tested by running the `runit/univariate_runtests.R` R file
+
+You will need to install **RUnit** package in order to make it run:
+```r
+install.packages('RUnit', dependencies = TRUE)
+```
+
+### Working example  
+
+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)  
+
+### News
+
+###### CHANGES IN VERSION 2.2.4  
+
+MINOR MODIFICATION  
+
+ * Internal minor modifications for building and testing  
+
+###### CHANGES IN VERSION 2.2.0  
+
+MAJOR MODIFICATION  
+
+ * ANOVA and Kruskal-Wallis: The p-values of the post-hoc tests (i.e. from pairwise comparisons) are now further corrected for multiple testing over all variables (previously, only the p-value of the -first- omnibus test was corrected over all variables)  
+
+MINOR MODIFICATION  
+
+ * All values in the 'dif', adjusted p-value, and 'sig' columns are now displayed (previously, the values were set to NA when the p-value of the omnibus test was not significant)  
+
+NEW FEATURE  
+
+ * Graphic: a single pdf file containing the graphics of all significant tests is now produced as '_figure.pdf' output: boxplots (respectively scatterplots with the regression line in red and the R2 value) are displayed when the factor of interest is qualitative (respectively quantitative). The corrected p-value is indicated in the title of each plot  
+
+###### CHANGES IN VERSION 2.1.4
+
+NEW FEATURE  
+
+ * 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)  
+
+INTERNAL MODIFICATION  
+
+ * Minor internal changes  
+
+###### CHANGES IN VERSION 2.1.2  
+
+INTERNAL MODIFICATION  
+
+ * Minor internal changes in .shed.yml for toolshed export
+
+###### CHANGES IN VERSION 2.1.1  
+
+INTERNAL MODIFICATION  
+
+ * Internal handling of 'NA' p-values (e.g. when intensities are identical in all samples).

tools/univariate/test-data/dataMatrix.tsv

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+dataMatrix	s1	s2	s3	s4	s5	s6	s7	s8	s9	s10	s11	s12	s13	s14	s15	s16	s17	s18	s19	s20	s21	s22	s23	s24	s25	s26	s27	s28	s29	s30	s31	s32
+v1	7.416640524	6.9916690517	7.3404441347	7.0128372669	7.1702617447	6.820858055	7.2648178466	6.9561684785	7.2966652122	7.2695129676	7.2695129676	6.7986507145	6.9749720403	6.7788745443	7.0791812822	7.3617278549	7.4281348102	6.967548023	7.2304489469	6.6608655728	6.9614211415	6.8959747875	7.1398791179	7.2201081142	7.1673173643	6.6857418281	7.1789769761	6.7788745443	6.7291648707	6.7466342768	6.8954226013	6.9454686344
+v2	7.4563660483	6.9014583759	7.3873898441	6.9599948859	7.2095150414	6.7007038037	7.3159703664	6.8876173566	7.3010300174	7.2966652122	7.3138672415	6.7275413384	6.9863238219	6.7435098431	7.1038037552	7.3838153839	7.4409090978	6.7737865181	7.2174839705	6.48995862	6.8494194752	6.8344207673	7.1238516736	7.212187631	7.2041200098	6.6910815806	7.2900346336	6.7427252098	6.7185017719	6.6180482014	6.8512584099	6.9329808726
+v3	6.8785218529	6.7839036507	6.9025468337	7.0086002143	6.9314579215	6.8129134235	6.8305887328	7.0374265378	6.8767950339	6.8457180799	6.7888751864	6.9929951426	7.0374265378	6.8215135939	7.0718820441	6.809559782	6.8122447637	6.7795965634	6.8129134235	6.9599948859	6.8014037786	6.7355989795	6.8075350957	6.9929951426	6.7686381752	6.9339932144	6.7611758884	6.9740509489	6.9768083831	6.7058637978	6.9790929462	6.7032914641
+v4	7.1303338007	7.1398791179	7.0899051467	7.110589744	6.9947569885	6.9978231244	7.0374265378	7.1003705796	6.9698816903	6.8048207468	6.8543061025	6.6655810848	6.705008045	6.7275413384	6.7442930614	6.9498777528	7.1583625223	7.2013971516	7.1673173643	6.9169800999	7.1003705796	7.0453230179	7.0606978781	7.1003705796	7.0492180614	6.7693773999	6.7774268949	6.9211661027	6.8561245047	6.9656720182	7.0086002143	6.9758911823
+v5	7.0530784819	6.99122612	7.0569048894	6.9698816903	6.8603380665	6.8375885014	6.9633155586	7.0170333811	7.0681858989	6.9633155586	6.95375974	6.7481881046	6.7686381752	6.8175654357	6.8394781102	7.0492180614	7.1038037552	7.0681858989	7.0755469979	6.7259117139	6.9339932144	6.8948697121	6.9464523141	7.0043214168	6.9009131223	6.6875290504	6.7634280684	6.7209858267	6.6454223676	6.7923917595	6.7902852344	6.8312297579
+v6	6.9876663096	7.0969100478	7.1072100036	7.0569048894	7.0000000434	6.9973864281	7.0644580267	7.0863598663	7.0043214168	6.9772662582	6.9434945654	6.9680157607	6.9556877984	7.1553360678	6.9454686344	6.9309490821	7.0086002143	7.0334237957	7.0086002143	6.9206450535	7.0043214168	6.9749720403	6.9489018098	6.9400182049	6.8750613213	6.9434945654	6.9057959343	6.9614211415	6.9518230838	6.9415114823	6.9304396457	6.9304396457

tools/univariate/test-data/output-variableMetadata.tsv

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+variableMetadata	sample_mean	qual_kruskal_fdr	qual_kruskal_sig	qual_kruskal_B.A_dif	qual_kruskal_C.A_dif	qual_kruskal_D.A_dif	qual_kruskal_C.B_dif	qual_kruskal_D.B_dif	qual_kruskal_D.C_dif	qual_kruskal_B.A_fdr	qual_kruskal_C.A_fdr	qual_kruskal_D.A_fdr	qual_kruskal_C.B_fdr	qual_kruskal_D.B_fdr	qual_kruskal_D.C_fdr	qual_kruskal_B.A_sig	qual_kruskal_C.A_sig	qual_kruskal_D.A_sig	qual_kruskal_C.B_sig	qual_kruskal_D.B_sig	qual_kruskal_D.C_sig
+v1	12620948.56	0.147579228303049	0	0.0827976191000008	-0.0378359353499995	-0.254400932999999	-0.12063355445	-0.3371985521	-0.21656499765	0.999945671392641	0.99999320349658	0.185342280966466	0.997174540126794	0.401201067449129	0.580170916884995	0	0	0	0	0	0
+v2	12661823.42	0.246364577097618	0	0.11547952005	-0.0981193892499999	-0.2877631538	-0.2135989093	-0.40324267385	-0.18964376455	0.999945671392641	0.99999320349658	0.291618067987092	0.997174540126794	0.401201067449129	0.890397531402986	0	0	0	0	0	0
+v3	7680621.526	0.293234285978368	0	-0.0292777863999998	-0.0806444136	-0.0392186484999995	-0.0513666272000002	-0.00994086209999967	0.0414257651000005	0.999945671392641	0.99999320349658	0.593281055056761	0.997174540126794	0.593281055056761	0.999155846185138	0	0	0	0	0	0
+v4	9901182.687	0.000819466212247517	1	-0.32058095905	0.00523271645000012	-0.1517188027	0.3258136755	0.16886215635	-0.15695151915	0.0133536911280914	0.99999320349658	0.185342280966466	0.00430289478770107	0.593281055056761	0.143731083414931	1	0	0	1	0	0
+v5	8311866.237	0.0115079177714078	1	-0.0839349800499996	-0.00516703969999988	-0.203697253750001	0.0787679403499997	-0.119762273700001	-0.198530214050001	0.999945671392641	0.99999320349658	0.0336157236420893	0.997174540126794	0.401201067449129	0.073221827596323	0	0	1	0	0	0
+v6	9792909.819	0.00429379409695042	1	-0.0988296785000005	-0.0710347295000009	-0.124705894050001	0.0277949489999996	-0.0258762155500003	-0.0536711645499999	0.535700151485478	0.99999320349658	0.00294595180681068	0.997174540126794	0.401201067449129	0.302648332248575	0	0	1	0	0	0

tools/univariate/test-data/sampleMetadata.tsv

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+sampleMetadata	quant	qual
+s1	56	A
+s2	24	A
+s3	35	A
+s4	32	A
+s5	54	A
+s6	53	A
+s7	30	A
+s8	20	A
+s9	41	B
+s10	34	B
+s11	44	B
+s12	43	B
+s13	52	B
+s14	46	B
+s15	51	B
+s16	36	B
+s17	31	C
+s18	25	C
+s19	40	C
+s20	50	C
+s21	22	C
+s22	29	C
+s23	49	C
+s24	19	C
+s25	55	D
+s26	39	D
+s27	45	D
+s28	26	D
+s29	23	D
+s30	42	D
+s31	33	D
+s32	21	D

tools/univariate/test-data/variableMetadata.tsv

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+variableMetadata	sample_mean
+v1	12620948.56
+v2	12661823.42
+v3	7680621.526
+v4	9901182.687
+v5	8311866.237
+v6	9792909.819

tools/univariate/test/.gitignore

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+*.tsv

tools/univariate/test/test-univ

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+#!/bin/bash
+
+# Constants {{{1
+################################################################
+
+PROG_PATH=$(dirname $0)
+
+# MAIN {{{1
+################################################################
+
+$PROG_PATH/../univariate_wrapper.R dataMatrix_in $PROG_PATH/../test-data/dataMatrix.tsv sampleMetadata_in $PROG_PATH/../test-data/sampleMetadata.tsv variableMetadata_in $PROG_PATH/../test-data/variableMetadata.tsv facC qual tesC kruskal adjC fdr thrN 0.05 variableMetadata_out $PROG_PATH/outputVariableMetadata.tsv
+
+if ! diff "$PROG_PATH/outputVariableMetadata.tsv" "$PROG_PATH/../test-data/output-variableMetadata.tsv" ; then
+	echo "Incorrect output variable metadata." >&2
+	exit 1
+fi

tools/univariate/univariate.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: pdfLaTeX
+
+BuildType: Makefile