Mercurial > repos > melpetera > batchcorrection
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author | melpetera |
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date | Thu, 14 Jan 2021 09:56:58 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BC/README.md Thu Jan 14 09:56:58 2021 +0000 @@ -0,0 +1,128 @@ +Signal drift and batch-effect correction +======================================== + +A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure + +Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/batch_correction.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/batch_correction). + +### Description + +**Version:** 3.0.0 +**Date:** 2020-10-02 +**Author:** Jean-Francois Martin (INRAE, AXIOM), Melanie Petera (INRAE, PFEM), Marion Landi (PFEM), Franck Giacomoni (INRAE, PFEM), and Etienne A. Thevenot (CEA, LIST) +**Email:** [jean-francois.martin(at)inrae.fr](mailto:jean-francois.martin@inrae.fr), [melanie.petera(at)inrae.fr](mailto:melanie.petera@inrae.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` +* Wrapper files: + + `batch_correction_3Lwrapper.R` + + `batch_correction_all_loess_wrapper.R` +* Script files: + + `batch_correction_3Lfct.R` + + `batch_correction_3Llauncher.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 + +Some functional tests are provided in Galaxy format (see XML wrapper and test-data folder). + +WIP: The code in the batch_correction_wrapper can be tested by running the `test/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 3.0.0 + +NEW FEATURES + + * Specific names for the 'sampleType', 'injectionOrder', and 'batch' from sampleMetadata are now available in a dedicated parameter section + * Addition of a sum of ions before/after plot for linear/lowess/loess methods + * Addition of a third option in "Null values" parameter (renamed "unconsistant values") in linear/lowess/loess methods + * linear/lowess/loess methods now handle NA in intensities and allow "blank" samples in the dataset + +INTERNAL MODIFICATIONS + + * XML optimisation using macros + * Output name changes + * linear/lowess/loess methods: disabling of RData output + * linear/lowess/loess methods: split of tool-linked code and script-linked one + * linear/lowess/loess methods: adjustments in the normalisation process to match matters linked to NA acceptance + * linear/lowess/loess methods: better handling of special characters in IDs and column names + +###### CHANGES IN VERSION 2.2.4 + +INTERNAL MODIFICATIONS + +Fixed bug for pool selection ("all_loess" methods) + +###### CHANGES IN VERSION 2.2.2 + +INTERNAL MODIFICATIONS + +Fixed bug for color plot ("all_loess" methods) + +###### CHANGES IN VERSION 2.2.0 + +NEW FEATURE + +Specific names for the 'sampleType', 'injectionOrder', and 'batch' from sampleMetadata can be selected by the user (for compatibility with the MTBLS downloader) + +##### 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)