Installation | Introduction | Walk through | Prerequisites | Loading the data | Loading the methylation and annotation data | The betaHMM workflow | Model parameter estimation | Summary of model parameters | DMC identification | Summary of the DMCs identified | Plot the density estimates of the model parameter estimates | DMR identification from DMCs identified | Summary of the DMRs identified | Plot to visualise the DMCs and DMRs | Threshold identification in DNA samples belonging to a specific condition | Plotting the results from threshold identification function
Package: betaHMM 1.9.0
Koyel Majumdar
betaHMM: A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Beta-Valued DNA Methylation Data
A novel approach utilizing a homogeneous hidden Markov model. And effectively model untransformed beta values. To identify DMCs while considering the spatial. Correlation of the adjacent CpG sites.
Authors:
betaHMM_1.9.0.tar.gz
betaHMM_1.9.0.zip(r-4.7)betaHMM_1.9.0.zip(r-4.6)betaHMM_1.9.0.zip(r-4.5)
betaHMM_1.9.0.tgz(r-4.6-any)betaHMM_1.9.0.tgz(r-4.5-any)
betaHMM_1.9.0.tar.gz(r-4.7-any)betaHMM_1.9.0.tar.gz(r-4.6-any)
betaHMM_1.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
betaHMM/json (API)
| # Install 'betaHMM' in R: |
| install.packages('betaHMM', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- annotation_data - MethylationEPIC manifest data.
- pca_methylation_data - Simulated DNA methylation data
- sample_annotation_file - MethylationEPIC manifest data.
- sample_methylation_file - Simulated DNA methylation data
On BioConductor:betaHMM-1.9.0(bioc 3.24)betaHMM-1.8.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
dnamethylationdifferentialmethylationimmunooncologybiomedicalinformaticsmethylationarraysoftwaremultiplecomparisonsequencingspatialcoveragegenetargethiddenmarkovmodelmicroarray
Last updated from:a81397575e. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 179 | ||
| linux-devel-x86_64 | OK | 598 | ||
| source / vignettes | OK | 417 | ||
| linux-release-x86_64 | OK | 565 | ||
| macos-release-arm64 | OK | 299 | ||
| macos-oldrel-arm64 | OK | 320 | ||
| windows-devel | OK | 522 | ||
| windows-release | OK | 492 | ||
| windows-oldrel | OK | 518 | ||
| wasm-release | OK | 162 |
Exports:AannotatedDataAUCbetaHMMbetaHMMResultsbetaHMMrunchromosome_numberdmc_identificationdmc_identification_rundmcResultsdmr_identificationdmr_identification_rundmrResultshidden_statesKllkmodel_parametersNphiplotRsummarytauthresholdthreshold_identificationthreshold_identification_runthreshold_Resultstreatment_groupuncertainty
Dependencies:abindBiobaseBiocGenericsclicodetoolscowplotcpp11DelayedArraydoParalleldplyrfarverforeachgenericsGenomicRangesggplot2gluegtableIRangesisobanditeratorslabelinglatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatspillarpkgconfigpROCpurrrR6RColorBrewerRcpprlangS4ArraysS4VectorsS7scalesSeqinfoSparseArraystringistringrSummarizedExperimenttibbletidyrtidyselectutf8vctrsviridisLitewithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Accessors for the betaHMM package. | A A,betaHMMResults-method A,NULL-method A,RangedSummarizedExperiment-method annotatedData annotatedData,betaHMMResults-method annotatedData,threshold_Results-method AUC AUC,dmcResults-method AUC,NULL-method AUC,RangedSummarizedExperiment-method chromosome_number chromosome_number,betaHMMResults-method chromosome_number,dmrResults-method chromosome_number,NULL-method chromosome_number,RangedSummarizedExperiment-method hidden_states hidden_states,betaHMMResults-method hidden_states,NULL-method hidden_states,RangedSummarizedExperiment-method hidden_states,threshold_Results-method K K,betaHMMResults-method K,dmcResults-method K,NULL-method K,RangedSummarizedExperiment-method K,threshold_Results-method llk llk,betaHMMResults-method llk,NULL-method llk,RangedSummarizedExperiment-method model_parameters model_parameters,NULL-method model_parameters,RangedSummarizedExperiment-method model_parameters,threshold_Results-method N N,betaHMMResults-method N,dmcResults-method N,NULL-method N,RangedSummarizedExperiment-method phi phi,betaHMMResults-method phi,NULL-method phi,RangedSummarizedExperiment-method phi,threshold_Results-method R R,betaHMMResults-method R,dmcResults-method R,NULL-method R,RangedSummarizedExperiment-method tau tau,betaHMMResults-method tau,NULL-method tau,RangedSummarizedExperiment-method threshold threshold,NULL-method threshold,RangedSummarizedExperiment-method threshold,threshold_Results-method treatment_group treatment_group,betaHMMResults-method treatment_group,dmcResults-method treatment_group,NULL-method treatment_group,RangedSummarizedExperiment-method uncertainty uncertainty,dmcResults-method uncertainty,NULL-method uncertainty,RangedSummarizedExperiment-method |
| MethylationEPIC manifest data. | annotation_data |
| HMM for beta valued DNA data | betaHMM betaHMM,data.frame,data.frame-method betaHMM,data.frame,GRanges-method betaHMM,data.frame,matrix-method betaHMM,data.frame,RangedSummarizedExperiment-method betaHMM,data.frame,RangedSummarizedExperiment.-method betaHMM,GRanges,data.frame-method betaHMM,GRanges,GRanges-method betaHMM,GRanges,matrix-method betaHMM,GRanges,RangedSummarizedExperiment-method betaHMM,matrix,data.frame-method betaHMM,matrix,GRanges-method betaHMM,matrix,matrix-method betaHMM,matrix,RangedSummarizedExperiment-method betaHMM,matrix,RangedSummarizedExperiment.-method betaHMM,RangedSummarizedExperiment,data.frame-method betaHMM,RangedSummarizedExperiment,GRanges-method betaHMM,RangedSummarizedExperiment,matrix-method betaHMM,RangedSummarizedExperiment,RangedSummarizedExperiment-method betaHMM,RangedSummarizedExperiment,RangedSummarizedExperiment.-method betaHMM-methods |
| betaHMMResults object and constructor | betaHMMResults betaHMMResults-class |
| The betaHMM model parameter estimation function | betaHMMrun |
| DMC identification from estimated betaHMM model parameters | dmc_identification dmc_identification,betaHMMResults-method dmc_identification-methods |
| DMC identification from estimated betaHMM model parameters | dmc_identification_run |
| dmcResults object and constructor | dmcResults dmcResults-class |
| DMR identification from DMCs identified | dmr_identification dmr_identification,data.frame-method dmr_identification,dmcResults-method dmr_identification,matrix-method dmr_identification-methods |
| DMR identification from DMCs identified | dmr_identification_run |
| dmrResults object and constructor | dmrResults dmrResults-class |
| Simulated DNA methylation data | pca_methylation_data |
| Visualize results from 'betaHMM'/ 'dmc_identification'/ 'threshold_identification' functions. | plot plot,betaHMMResults-method plot,dmcResults-method plot,threshold_Results-method plot-methods |
| MethylationEPIC manifest data. | sample_annotation_file |
| Simulated DNA methylation data | sample_methylation_file |
| Summarize results from the three betaHMM workflow functions | summary summary,betaHMMResults-method summary,dmcResults-method summary,dmrResults-method summary-methods |
| HMM for beta valued DNA data for a single treatment condition | threshold_identification threshold_identification,data.frame-method threshold_identification,matrix-method threshold_identification-methods |
| Threshold indentification function | threshold_identification_run |
| threshold_Results object and constructor | threshold_Results threshold_Results-class |
