Package: DMRScan 1.29.0
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_1.29.0.tar.gz
DMRScan_1.29.0.zip(r-4.5)DMRScan_1.29.0.zip(r-4.4)DMRScan_1.29.0.zip(r-4.3)
DMRScan_1.29.0.tgz(r-4.4-any)DMRScan_1.29.0.tgz(r-4.3-any)
DMRScan_1.29.0.tar.gz(r-4.5-noble)DMRScan_1.29.0.tar.gz(r-4.4-noble)
DMRScan_1.29.0.tgz(r-4.4-emscripten)DMRScan_1.29.0.tgz(r-4.3-emscripten)
DMRScan.pdf |DMRScan.html✨
DMRScan/json (API)
NEWS
| # 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
- DMRScan.methylationData - DMRScan
- DMRScan.phenotypes - DMRScan
On BioConductor:DMRScan-1.29.0(bioc 3.21)DMRScan-1.28.0(bioc 3.20)
softwaretechnologysequencingwholegenome
Last updated 2 months agofrom:b96365d64c. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | NOTE | Nov 29 2024 |
| R-4.5-linux | NOTE | Nov 29 2024 |
| R-4.4-win | NOTE | Nov 29 2024 |
| R-4.4-mac | NOTE | Nov 29 2024 |
| R-4.3-win | OK | Nov 29 2024 |
| R-4.3-mac | OK | Nov 29 2024 |
Exports:dmrscanestimateWindowThresholdmakeCpGgenesmakeCpGregions
Dependencies:askpassBiocGenericscurlgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelatticeMASSMatrixmimemvtnormopensslR6RcppRcppRollS4VectorssysUCSC.utilsXVectorzlibbioc
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 |
