Checking/formatting the sample and variable names of the dataMatrix, sampleMetadata, and variableMetadata files
A Galaxy module from the Workflow4metabolomics infrastructure
Status: 
Version: 3.0.0
Date: 2018-01-10
Author: Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)
Email: 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
Licence: CeCILL
Reference histories:
W4M00001a_sacurine-subset-statistics, W4M00001b_sacurine_complete,
W4M00002_sacurine_mtbls2, W4M00003_sacurine_diaplasma
Funding: Agence Nationale de la Recherche (MetaboHUB national infrastructure for metabolomics and fluxomics, ANR-11-INBS-0010 grant)
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Configuration file:
checkformat_config.xml -
Image file:
static/images/checkformat_workflowPositionImage.png -
Wrapper file:
checkformat_wrapper.R -
R packages
- batch from CRAN
install.packages("batch", dep=TRUE)
The code in the wrapper can be tested by running the runit/checkformat_tests.R R file
You will need to install RUnit package in order to make it run:
install.packages('RUnit', dependencies = TRUE)See the W4M00001a_sacurine-subset-statistics, W4M00001b_sacurine-complete, W4M00002_mtbls2, or W4M00003_diaplasma shared histories in the Shared Data/Published Histories menu (https://galaxy.workflow4metabolomics.org/history/list_published)
NEW FEATURES
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Automated re-ordering (if necessary) of sample and/or variable names from dataMatrix based on sampleMetadata and variableMetadata
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New argument to make sample and variable names syntactically valid
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Output of dataMatrix, sampleMetadata, and variableMetadata files, whether they have been modified or not
INTERNAL MODIFICATION
- Minor internal modifications
INTERNAL MODIFICATION
- Creating tests for R code