Abstract | Motivation | Methods | Data Set | Work flow and use of DMRScan | Data inputs | Example data | Test statistics | Clustering of the test statics into "Chunks" | DMRScan | Calculating window thresholds | Identifying Differentially Methylated Regions | Estimating window thresholds with an ARIMA model using MCMC | References
Package: DMRScan 1.35.0
Christian M Page
DMRScan: Detection of Differentially Methylated Regions
This package detects significant differentially methylated regions (for both qualitative and quantitative traits), using a scan statistic with underlying Poisson heuristics. The scan statistic will depend on a sequence of window sizes (# of CpGs within each window) and on a threshold for each window size. This threshold can be calculated by three different means: i) analytically using Siegmund et.al (2012) solution (preferred), ii) an important sampling as suggested by Zhang (2008), and a iii) full MCMC modeling of the data, choosing between a number of different options for modeling the dependency between each CpG.
Authors:
DMRScan_1.35.0.tar.gz
DMRScan_1.35.0.zip(r-4.7)DMRScan_1.35.0.zip(r-4.6)DMRScan_1.35.0.zip(r-4.5)
DMRScan_1.35.0.tgz(r-4.6-any)DMRScan_1.35.0.tgz(r-4.5-any)
DMRScan_1.35.0.tar.gz(r-4.7-any)DMRScan_1.35.0.tar.gz(r-4.6-any)
DMRScan_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DMRScan/json (API)
| # Install 'DMRScan' in R: |
| install.packages('DMRScan', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/christpa/dmrscan/issues
Datasets:
- DMRScan.methylationData - DMRScan
- DMRScan.phenotypes - DMRScan
On BioConductor:DMRScan-1.35.0(bioc 3.24)DMRScan-1.34.0(bioc 3.23)
softwaretechnologysequencingwholegenome
Last updated from:63e5f092d6. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 202 | ||
| linux-devel-x86_64 | NOTE | 433 | ||
| source / vignettes | OK | 232 | ||
| linux-release-x86_64 | NOTE | 352 | ||
| macos-release-arm64 | NOTE | 292 | ||
| macos-oldrel-arm64 | NOTE | 174 | ||
| windows-devel | NOTE | 312 | ||
| windows-release | NOTE | 300 | ||
| windows-oldrel | NOTE | 423 | ||
| wasm-release | OK | 125 |
Exports:dmrscanestimateWindowThresholdmakeCpGgenesmakeCpGregions
Dependencies:BiocGenericsgenericsGenomicRangesIRangeslatticeMASSMatrixmvtnormRcppRcppRollS4VectorsSeqinfo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| DMR Scan function | dmrscan |
| DMRScan: An R-package for identification of Differentially Metylated Regions | DMRScan_package-package DMRScan_package |
| DMRScan | DMRScan.methylationData |
| DMRScan | DMRScan.phenotypes |
| EstimateWindowThresholds | estimateThreshold estimateWindowThreshold |
| Cluster | makeCpGgenes |
| Cluster | makeCpGregions |
| Method Fixed window size scan for a sequence of window sizes | manyWindowSizeScanner manyWindowSizeScanner,GRanges-method manyWindowSizeScanner,GRangesList-method St |
| Method Fixed window size scan for one window size | oneWindowSizeScanner oneWindowSizeScanner,GRanges-method oneWindowSizeScanner,GRangesList-method Rt Rt,GRanges-method Rt,GRangesList-method |
