Licensing | Citing | Introduction | Loading methInheritSim package | Description of the simulation process | Simulated control dataset | Simulated case dataset | Case study | The simulated dataset | The simulation | Files generated by the simulation | Synthetic chromosome in GRanges format ("syntheticChr" prefix) | Simulation information in GRanges format ("simData" prefix) | Information about DMS state ("stateDiff" prefix) | Files related to saveGRanges parameter | Raw methylation data for all samples in GRanges format ("methylGR" prefix) | Information about controls and cases ("treatment" prefix) | Files related to saveMethylKit parameter | Raw methylation data in methylRaw format ("methylObj" prefix) | Files related to runAnalysis parameter | Methylation events present in multiple samples in methylBase format ("meth" prefix) | Differential methylation statistics in methylDiff format ("methDiff" prefix) | Conclusion
Package: methInheritSim 1.35.0
Pascal Belleau
methInheritSim: Simulating Whole-Genome Inherited Bisulphite Sequencing Data
Simulate a multigeneration methylation case versus control experiment with inheritance relation using a real control dataset.
Authors:
methInheritSim_1.35.0.tar.gz
methInheritSim_1.35.0.zip(r-4.7)methInheritSim_1.35.0.zip(r-4.6)methInheritSim_1.35.0.zip(r-4.5)
methInheritSim_1.35.0.tgz(r-4.6-any)methInheritSim_1.35.0.tgz(r-4.5-any)
methInheritSim_1.35.0.tar.gz(r-4.7-any)methInheritSim_1.35.0.tar.gz(r-4.6-any)
methInheritSim_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
methInheritSim/json (API)
| # Install 'methInheritSim' in R: |
| install.packages('methInheritSim', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/belleau/methinheritsim/issues
Datasets:
- dataSimExample - A 'list' containing methylation information used by some internal functions (for demo purpose.
- samplesForChrSynthetic - All samples information, formated by 'methylKit', in a 'methylBase' format (for demo purpose).
On BioConductor:methInheritSim-1.35.0(bioc 3.24)methInheritSim-1.34.0(bioc 3.23)
biologicalquestionepigeneticsdnamethylationdifferentialmethylationmethylseqsoftwareimmunooncologystatisticalmethodwholegenomesequencingbisulphite-sequencinginheritancemethylationsimulation
Last updated from:17b462cd6d. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 211 | ||
| linux-devel-x86_64 | NOTE | 413 | ||
| source / vignettes | OK | 352 | ||
| linux-release-x86_64 | NOTE | 463 | ||
| macos-release-arm64 | NOTE | 252 | ||
| macos-oldrel-arm64 | NOTE | 195 | ||
| windows-devel | NOTE | 330 | ||
| windows-release | NOTE | 311 | ||
| windows-oldrel | NOTE | 331 | ||
| wasm-release | OK | 194 |
Exports:runSim
Dependencies:abindaskpassbbmlebdsmatrixBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopscigarilloclicodacodetoolscpp11crayoncurldata.tableDelayedArrayemdbookexpmfarverfastsegformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2gluegtablegtoolshttrIRangesisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmethylKitmgcvmimemsmmvtnormnlmenumDerivopensslpillarpkgconfigplyrqvalueR.methodsS3R.ooR.utilsR6RColorBrewerRcppRCurlreshape2restfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystatmodstringistringrSummarizedExperimentsurvivalsystibbleutf8vctrsviridisLitewithrXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| methInheritSim: Simulating Whole-Genome Inherited Bisulphite Sequencing Data | methInheritSim-package methInheritSim |
| A 'list' containing methylation information used by some internal functions (for demo purpose. | dataSimExample |
| Simulate a multigeneration methylation experiment with inheritance | runSim |
| All samples information, formated by 'methylKit', in a 'methylBase' format (for demo purpose). | samplesForChrSynthetic |
