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# DMRScan R package for detection of differentially methylated regions with adjustment for multiple testing # Important Info ## Authors CM Page, L Vos, BK Andreasen ## Package structure The function `DMRScan()` requires three key inputs; - a vector of test statistics for each CpG site, - the corresponding positions (chromosome and bp position). Additional inputs are the - maximum allowed distance within a region - the minimum number of CpGs within a region. ### Installation For a stable release from Bioconductor use ```R if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("DMRScan") ``` For the developmental version from Github, use ```R devtools::install_github("christpa/DMRScan") ``` Requred R-packages for DMRScan are: * Matrix * MASS * RcppRoll * GenomicRanges * IRanges * methods * mvtnorm * stats * parallel ======= ### Usage Please see the vignette. # Citation To cite the DMRScan package in publications please use: Page, C. M., Vos, L., Rounge, T. B., Harbo, H. F., & Andreassen, B. K. (2018). Assessing genome-wide significance for the detection of differentially methylated regions. *Statistical applications in genetics and molecular biology.* A BibTeX entry for LaTeX users is ```BibTeX @article{DMR_paper, title={Assessing genome-wide significance for the detection of differentially methylated regions}, author={Page, Christian M and Vos, Linda and Rounge, Trine B and Harbo, Hanne F and Andreassen, Bettina K}, journal={Statistical applications in genetics and molecular biology}, year={2018}, publisher={De Gruyter} }``` ```{r} sessionInfo() ``` ``` R version 3.4.2 (2017-09-28) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.6 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] DMRScan_0.01.02 loaded via a namespace (and not attached): [1] Rcpp_0.12.13 mvtnorm_1.0-6 lattice_0.20-35 [4] IRanges_2.10.5 RcppRoll_0.2.2 bitops_1.0-6 [7] MASS_7.3-47 GenomeInfoDb_1.12.3 grid_3.4.2 [10] stats4_3.4.2 zlibbioc_1.22.0 XVector_0.16.0 [13] S4Vectors_0.14.7 Matrix_1.2-11 RCurl_1.95-4.8 [16] parallel_3.4.2 compiler_3.4.2 BiocGenerics_0.22.1 [19] GenomicRanges_1.28.6 GenomeInfoDbData_0.99.0 ``` End of README