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# BPRMeth: modelling DNA methylation profiles [![BioC status](]( [![DOI](]( The aim of `BPRMeth` is to extract higher order features associated with the shape of methylation profiles across a defined genomic region. Using these higher order features across promoter-proximal regions, BPRMeth provides a powerful machine learning predictor of gene expression. Check the vignette on how to use the package. Modelling details for the different models can be found online: []( The original implementation has now been enhanced in two important ways: we introduced a fast, __variational inference__ approach which enables the quantification of Bayesian posterior confidence measures on the model, and we adapted the method to use several observation models, making it suitable for a diverse range of platforms including __single-cell__ and __bulk__ sequencing experiments and __methylation arrays__. ## Installation To get the latest development version from Github: ```R # install.packages("devtools") devtools::install_github("andreaskapou/BPRMeth", build_vignettes = TRUE) ``` Or install from the stable release version from Bioconductor ```R ## try http:// if https:// URLs are not supported if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("BPRMeth") ``` You can the check the vignette on how to use the package: ```R browseVignettes("BPRMeth") ``` ## Clang / fopenmp error for Mac users If you get the following error when installing the package: `clang: error: unsupported option '-fopenmp'` try the following: ```R brew install llvm brew install boost brew install homebrew/science/hdf5 --enable-cxx mkdir -p ~/.R vim ~/.R/Makevars ## Paste the following commands # The following statements are required to use the clang4 binary CC=/usr/local/clang4/bin/clang CXX=/usr/local/clang4/bin/clang++ CXX11=/usr/local/clang4/bin/clang++ CXX14=/usr/local/clang4/bin/clang++ CXX17=/usr/local/clang4/bin/clang++ CXX1X=/usr/local/clang4/bin/clang++ LDFLAGS=-L/usr/local/clang4/lib # End clang4 inclusion statements ``` These commands will point R to the new version of clang. ## `BPRMeth` workflow The diagram below shows an overview of the pre-processing and analysis workflow in `BPRMeth`, together with example output graphs. ![Diagram outlining the schematic workflow of BPRMeth (left) with example output graphs (right).](inst/figures/bprmeth-workflow.png) ## Citation Kapourani, C.-A. and Sanguinetti, G. (2016). Higher order methylation features for clustering and prediction in epigenomic studies. Bioinformatics 32 (17), i405-i412. **(Best Paper Award in ECCB 2016)**.