Name: qualitymetrics
Owner: Workflow4Metabolomics
Description: Metrics and graphics to check the quality of the data
Created: 2016-07-26 15:13:44.0
Updated: 2016-07-26 15:17:05.0
Pushed: 2018-01-11 18:02:08.0
Homepage: null
Size: 573
Language: R
GitHub Committers
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A Galaxy module from the Workflow4metabolomics infrastructure
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)
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
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/qualitymetrics_runtests.R
R file
You will need to install RUnit package in order to make it run:
all.packages('RUnit', dependencies = TRUE)
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
MINOR MODIFICATION
INTERNAL MODIFICATION
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
INTERNAL MODIFICATION