Mercurial > repos > melpetera > batchcorrection
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author | melpetera |
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date | Thu, 14 Jan 2021 09:56:58 +0000 |
parents | 73892ef177e3 |
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--- a/batchcorrection-57edfd3943ab/README.md Tue May 02 09:47:22 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,93 +0,0 @@ -Signal drift and batch-effect correction -======================================== - -A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure - -Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/batchcorrection.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/batchcorrection). - -### Description - -**Version:** 2.1.2 -**Date:** 2017-04-30 -**Author:** Jean-François Martin (INRA, AXIOM), Mélanie Pétéra (INRA, PFEM), Marion Landi (INRA, PFEM), Franck Giacomoni (INRA, PFEM), and Etienne A. Thévenot (CEA, LIST) -**Email:** [jean-francois.martin(at)toulouse.inra.fr](mailto:jean-francois.martin@toulouse.inra.frr), [melanie.petera(at)clermont.inra.fr](mailto:melanie.petera@clermont.inra.fr), [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) -**Citation:** -**Licence:** CeCILL -**Reference history:** [W4M00001_Sacurine-statistics; DOI:10.15454/1.4811121736910142E12](http://dx.doi.org/10.15454/1.4811121736910142E12) and [W4M00002_Sacurine-comprehensive; DOI:10.15454/1.481114233733302E12](http://dx.doi.org/10.15454/1.481114233733302E12) -**Funding:** Agence Nationale de la Recherche ([MetaboHUB](http://www.metabohub.fr/index.php?lang=en&Itemid=473) national infrastructure for metabolomics and fluxomics, ANR-11-INBS-0010 grant) - -### Installation - -* Configuration files: - + `batch_correction.xml` (for the "Batch Correction" module) - + `determine_bc.xml` (for the "Determine Batch Correction" module) -* Image files: - + `static/images/batch_correction.png` - + `static/images/determine_batch_correction.png` - + `static/images/pdf_plotsituation.png` - + `static/images/Vdk_pdf1.png` - + `static/images/Vdk_pdf2.png` -* Wrapper files: - + `batch_correction_wrapper.R` - + `batch_correction_all_loess_wrapper.R` -* Script files: - + `Normalisation_QCpool.r` - + `batch_correction_all_loess_script.R` -* R packages - + **batch** from CRAN - - ```r - install.packages("batch", dep=TRUE) - ``` - - + **ade4** from CRAN - - ```r - install.packages("ade4", dep=TRUE) - ``` - - + **pcaMethods** from Bioconductor - - ```r - source("http://www.bioconductor.org/biocLite.R") - biocLite("pcaMethods") - ``` - - + **ropls** from Bioconductor - - ```r - source("http://www.bioconductor.org/biocLite.R") - biocLite("ropls") - ``` - -### Tests - -The code in the batch_correction_wrapper can be tested by running the `runit/batchcorrection_runtests.R` R file - -You will need to install **RUnit** package in order to make it run: -```r -install.packages('RUnit', dependencies = TRUE) -``` - -### Working example - -See the reference histories [W4M00001_Sacurine-statistics; DOI:10.15454/1.4811121736910142E12](http://dx.doi.org/10.15454/1.4811121736910142E12) and [W4M00002_Sacurine-comprehensive; DOI:10.15454/1.481114233733302E12](http://dx.doi.org/10.15454/1.481114233733302E12) - - -### News - -##### CHANGES IN VERSION 2.1.2 - -INTERNAL MODIFICATIONS - - * Minor modifications in config file - -##### CHANGES IN VERSION 2.1.0 - -INTERNAL MODIFICATIONS - - * For PCA figure display only ("all_loess_" options): missing values are set to the minimum value before PCA computation is performed (with svd) - - * Additional running and installation tests added with planemo, conda, and travis - - * Modification of the 'all_loess_wrapper.R' file to handle 'ropls' package versions of 1.3.15 and above (i.e. after switching to S4 classes) \ No newline at end of file