GitHub - christpa/DMRScan: R package for detection of differentially methylated regions with adjustment for multiple testing (original) (raw)

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

if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("DMRScan")

For the developmental version from Github, use

devtools::install_github("christpa/DMRScan")

Requred R-packages for DMRScan are:

• Matrix
• MASS
• RcppRoll
• GenomicRanges
• IRanges
• methods
• mvtnorm
• stats
• parallel

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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

@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} }```

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