If all package dependencies were installed, you will be able to install the MetaboAnalylstR 2.0.
Get report file from metaboanalyst manual#
The package documentation, including the vignettes for each module and user manual is available within the downloaded R package file. MetaboAnalystR 2.0 is freely available from GitHub. Pacman::p_load(Rserve, ellipse, scatterplot3d, Cairo, randomForest, caTools, e1071, som, impute, pcaMethods, RJSONIO, ROCR, globaltest, GlobalAncova, Rgraphviz, preprocessCore, genefilter, pheatmap, SSPA, sva, Rcpp, pROC, data.table, limma, car, fitdistrplus, lars, Hmisc, magrittr, methods, xtable, pls, caret, lattice, igraph, gplots, KEGGgraph, reshape, RColorBrewer, tibble, siggenes, plotly, xcms, CAMERA, fgsea, MSnbase) Step 2. A printed message will appear informing you whether or not any R packages were installed.įunction to download packages: metanr_packages R 3.5.1). To install package dependencies, there are two options:Įnter the R function (metanr_packages) and then use the function. Ensure that you are able to download packages from bioconductor. To use MetaboAnalystR 2.0, first install all package dependencies. In this vignette, we perform end-to-end metabolomics data analysis on a subset of clinical IBD samples. To demonstrate this new functionality, we provide the "MetaboAnalystR 2.0 Workflow: From Raw Spectra to Biological Insights" vignette, available here as a PDF. In addition to an efficient implementation of the mummichog algorithm (PMID: 23861661), we have added a new method to support pathway activity prediction based on the well-established GSEA algorithm (PMID: 16199517). Second, we have enhanced support for functional interpretation directly from m/z peaks. Therefore, we have implemented comprehensive support for raw LC-MS spectral data processing including peak picking, peak alignment and peak annotations leveraging the functionality of the xcms (PMIDs: 16448051, 19040729, and 20671148 version 3.4.4) and CAMERA (PMID: 22111785 version 1.38.1) R packages. First, raw spectral processing - the previous version offered very limited support for raw spectra processing and peak annotation. With version 2.0, we aim to address two important gaps left in its previous version. After installing and loading the package, users will be able to reproduce the same results from their local computers using the corresponding R command history downloaded from MetaboAnalyst, thereby achieving maximum flexibility and reproducibility. The package is synchronized with the MetaboAnalyst web server. MetaboAnalystR 2.0 contains the R functions and libraries underlying the popular MetaboAnalyst web server, including > 500 functions for metabolomic data analysis, visualization, and functional interpretation. MetaboAnalystR 2.0: From Raw Spectra to Biological Insights Description
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