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] Rcpp0.12.13 mvtnorm1.0-6 lattice0.20-35
[4] IRanges2.10.5 RcppRoll0.2.2 bitops1.0-6
[7] MASS7.3-47 GenomeInfoDb1.12.3 grid3.4.2
[10] stats43.4.2 zlibbioc1.22.0 XVector0.16.0
[13] S4Vectors0.14.7 Matrix1.2-11 RCurl1.95-4.8
[16] parallel3.4.2 compiler3.4.2 BiocGenerics0.22.1
[19] GenomicRanges1.28.6 GenomeInfoDbData0.99.0 ```

End of README