Metrics and graphics to assess the quality of the data

A Galaxy module from the Workflow4metabolomics infrastructure

Status: .

Description

Version: 2.2.8
Date: 2018-01-11
Author: Marion Landi (INRA, PFEM), Mélanie Pétéra (INRA, PFEM), and Etienne A. Thévenot (CEA, LIST)
Email: melanie.petera(at)clermont.inra.fr, etienne.thevenot(at)cea.fr
Citation:
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:
  • qualitymetrics_config.xml
• Image files:
  • static/images/QualityControl.png
  • static/images/qualitymetrics_workingExampleImage.png
• Wrapper file:
  • qualitymetrics_wrapper.R
• Script file:
  • qualitymetrics_script.R
• R packages

  • batch from CRAN

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

  • ropls from Bioconductor

    source("http://www.bioconductor.org/biocLite.R")  
    biocLite("ropls")      

Tests

The code in the wrapper can be tested by running the runit/qualitymetrics_runtests.R R file

You will need to install RUnit package in order to make it run:

install.packages('RUnit', dependencies = TRUE)

News

CHANGES IN VERSION 2.2.8

MINOR MODIFICATION

In the case of a distinct sample order between dataMatrix and sampleMetadata, the sample order from the dataMatrix is matched to sampleMetadata internally for the computations and graphics without modifying the order in the sampleMetadata output (a warning is generated in the information file); to get the re-ordered dataMatrix as output, please use the Check Format module

CHANGES IN VERSION 2.2.6

MINOR MODIFICATION

• Graphic (pool_CV inferior to 30% metric): pools with a NaN value are now counted as having a value superior to 30% (to avoid generating a final NA metric value)

CHANGES IN VERSION 2.2.4

INTERNAL MODIFICATION

• Additional running and installation tests added with planemo, conda, and travis

CHANGES IN VERSION 2.2.3

INTERNAL MODIFICATION

• Modifications of the 'qualitymetrics_script.R' file to handle the recent 'ropls' package versions (i.e. 1.3.15 and above) which use S4 classes

• Creating tests for the R code

CHANGES IN VERSION 2.2.2

INTERNAL MODIFICATION

• Minor internal modification