workflow4metabolomics/univariate

Name: univariate

Owner: Workflow4Metabolomics

Description: Univariate parametric and non-parametric hypothesis testing with correction for multiple testing

Created: 2016-05-21 21:34:44.0

Updated: 2016-05-21 21:37:39.0

Pushed: 2018-01-11 15:14:50.0

Homepage: null

Size: 348

Language: R

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README

Univariate parametric and non-parametric hypothesis testing with correction for multiple testing

A Galaxy module from the Workflow4metabolomics infrastructure

Status: .

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; etienne.thevenot(at)cea.fr
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
Reference history: W4M00001a_sacurine-subset-statistics, W4M00004_mtbls1
Licence: CeCILL
Funding: Agence Nationale de la Recherche (MetaboHUB 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
  

  all.packages("batch", dep=TRUE)  
  

• PMCMR from CRAN
  

  all.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:

all.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).