# 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
