Name: multivariate
Owner: Workflow4Metabolomics
Description: PCA, PLS(-DA), and OPLS(-DA)
Created: 2016-05-15 16:06:11.0
Updated: 2016-05-15 16:10:41.0
Pushed: 2017-10-26 14:32:41.0
Homepage: null
Size: 1286
Language: R
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A Galaxy module from the Workflow4metabolomics infrastructure
Version: 2.3.8
Date: 2016-10-21
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 history: W4M00001a_sacurine-subset-statistics, W4M00001b_sacurine_complete
Funding: Agence Nationale de la Recherche (MetaboHUB national infrastructure for metabolomics and fluxomics, ANR-11-INBS-0010 grant)
Configuration file: multivariate_config.xml
Image files:
static/images/multivariate_workflowPositionImage.png
static/images/multivariate_workingExampleImage.png
Wrapper file: multivariate_wrapper.R
R packages
batch from CRAN
all.packages("batch", dep=TRUE)
ropls from Bioconductor
ce("http://www.bioconductor.org/biocLite.R")
Lite("ropls")
The code in the wrapper can be tested by running the runit/multivariate_runtests.R
R file
You will need to install RUnit package in order to make it run:
all.packages('RUnit', dependencies = TRUE)
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)
MINOR MODIFICATION
INTERNAL MODIFICATION
INTERNAL MODIFICATION
INTERNAL MODIFICATION
multivariate_wrapper.R
file to handle ropls package versions of 1.3.15 and above (i.e. after switching to S4 classes)NEW FEATURES