workflow4metabolomics/transformation

Name: transformation

Owner: Workflow4Metabolomics

Description: Transformation of the dataMatrix intensity values

Created: 2016-07-27 11:22:42.0

Updated: 2016-07-27 11:27:47.0

Pushed: 2017-08-03 14:47:34.0

Homepage: null

Size: 528

Language: R

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README

Transformation of the data matrix

A Galaxy module from the Workflow4metabolomics infrastructure

Status: .

Description

Version: 2.2.0
Date: 2016-08-04
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: W4M00001b_sacurine_complete
Funding: Agence Nationale de la Recherche (MetaboHUB national infrastructure for metabolomics and fluxomics, ANR-11-INBS-0010 grant)

Installation

• Configuration file: transformation_config.xml
  
• Image files: static/images/transformation_workflowPositionImage.png
  
• Wrapper file: transformation_wrapper.R
  
• R packages
  
  • batch from CRAN
    

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

Tests

The code in the wrapper can be tested by running the runit/transformation_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 W4M00001b_sacurine-complete or W4M00002_mtbls2 shared histories in the Shared Data/Published Histories menu (https://galaxy.workflow4metabolomics.org/history/list_published)

News

CHANGES IN VERSION 2.2.0

NEW FEATURE

• Square root transformation now available
  

CHANGES IN VERSION 2.0.2

INTERNAL MODIFICATION

• Creating tests for R code