Mercurial > repos > recetox > ramclustr_csv

annotate test-data/metadata_xcms_2.txt @ 3:61035548f46c draft default tip

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3479dea72f19e42832d30cda4283e56e81dd96d5"
author recetox
date Mon, 07 Jun 2021 15:13:41 +0000
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61035548f46c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3479dea72f19e42832d30cda4283e56e81dd96d5"
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1 Raw mass spectrometry data were processed using an R based workflow for feature detection, retention time alignment, feature grouping, peak filling, feature clustering. XCMS(v.3.10.2)was used for feature detection and retention time alighment. Processing was performed using R(v.R Core Team 2020). Feature data was input as an xcms object with ramclustR parameter settings of st = 3.92 sr = 0.5 and maxt = 78.4.RAMClustR (version 1.1.0) was utilized to cluster features into spectra (Broeckling 2014). The feature similarity matrix was clustered using fastcluster package heirarchical clustering method using the average method. The dendrogram was cut using the cutreeDynamicTree function from the dynamicTreeCut package. Cutting parameters were set to minModuleSize = 2, hmax = 0.3, and deepSplit = FALSE.
61035548f46c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3479dea72f19e42832d30cda4283e56e81dd96d5"
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61035548f46c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3479dea72f19e42832d30cda4283e56e81dd96d5"
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3 5881 features were collapsed into 949 spectra.
61035548f46c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3479dea72f19e42832d30cda4283e56e81dd96d5"
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61035548f46c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3479dea72f19e42832d30cda4283e56e81dd96d5"
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5 (Broeckling 2014): Broeckling CD, Afsar FA, Neumann S, Ben-Hur A, Prenni JE. RAMClust: a novel feature clustering method enables spectral-matching-based annotation for metabolomics data. Anal Chem. 2014. 86(14):6812-7.
61035548f46c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3479dea72f19e42832d30cda4283e56e81dd96d5"
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61035548f46c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3479dea72f19e42832d30cda4283e56e81dd96d5"
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7 R Core Team: R Core Team (2020). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria, https://www.R-project.org/.
61035548f46c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3479dea72f19e42832d30cda4283e56e81dd96d5"
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61035548f46c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3479dea72f19e42832d30cda4283e56e81dd96d5"
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9 R Core Team (2020). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria, https://www.R-project.org/.