Mercurial > repos > melpetera > batchcorrection
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author | melpetera |
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date | Tue, 02 May 2017 09:47:22 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/batchcorrection-57edfd3943ab/README.md Tue May 02 09:47:22 2017 -0400 @@ -0,0 +1,93 @@ +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