Package: betaHMM 1.3.0

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:Koyel Majumdar [cre, aut], Romina Silva [aut], Antoinette Sabrina Perry [aut], Ronald William Watson [aut], Isobel Claire Gorley [aut], Thomas Brendan Murphy [aut], Florence Jaffrezic [aut], Andrea Rau [aut]

betaHMM_1.3.0.tar.gz
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betaHMM.pdf |betaHMM.html✨
betaHMM/json (API)
NEWS

# Install 'betaHMM' in R:
install.packages('betaHMM', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On BioConductor:betaHMM-1.3.0(bioc 3.21)betaHMM-1.2.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

dnamethylationdifferentialmethylationimmunooncologybiomedicalinformaticsmethylationarraysoftwaremultiplecomparisonsequencingspatialcoveragegenetargethiddenmarkovmodelmicroarray

4.30 score 106 downloads 29 exports 69 dependencies

Last updated 22 days agofrom:be89a3fc18. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-winWARNINGNov 18 2024
R-4.5-linuxWARNINGNov 18 2024
R-4.4-winWARNINGNov 18 2024
R-4.4-macWARNINGNov 18 2024
R-4.3-winWARNINGNov 18 2024
R-4.3-macWARNINGNov 18 2024

Exports:AannotatedDataAUCbetaHMMbetaHMMResultsbetaHMMrunchromosome_numberdmc_identificationdmc_identification_rundmcResultsdmr_identificationdmr_identification_rundmrResultshidden_statesKllkmodel_parametersNphiplotRsummarytauthresholdthreshold_identificationthreshold_identification_runthreshold_Resultstreatment_groupuncertainty

Dependencies:abindaskpassBiobaseBiocGenericsclicodetoolscolorspacecowplotcpp11crayoncurlDelayedArraydoParalleldplyrfansifarverforeachgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobanditeratorsjsonlitelabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigplyrpROCpurrrR6RColorBrewerRcpprlangS4ArraysS4VectorsscalesSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

betaHMM package: Quick-start guide

Koyel Majumdar, Isobel Claire Gormley, Thomas Brendan Murphy, Romina Silva, Antoinette Sabrina Perry, Ronald William Watson, Florence Jaffrézic, Andrea Rau

Rendered frombetaHMM.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2023-11-22
Started: 2023-10-09

Readme and manuals

Help Manual

Help pageTopics
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 databetaHMM 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 constructorbetaHMMResults betaHMMResults-class
The betaHMM model parameter estimation functionbetaHMMrun
DMC identification from estimated betaHMM model parametersdmc_identification dmc_identification,betaHMMResults-method dmc_identification-methods
DMC identification from estimated betaHMM model parametersdmc_identification_run
dmcResults object and constructordmcResults dmcResults-class
DMR identification from DMCs identifieddmr_identification dmr_identification,data.frame-method dmr_identification,dmcResults-method dmr_identification,matrix-method dmr_identification-methods
DMR identification from DMCs identifieddmr_identification_run
dmrResults object and constructordmrResults dmrResults-class
Simulated DNA methylation datapca_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 datasample_methylation_file
Summarize results from the three betaHMM workflow functionssummary summary,betaHMMResults-method summary,dmcResults-method summary,dmrResults-method summary-methods
HMM for beta valued DNA data for a single treatment conditionthreshold_identification threshold_identification,data.frame-method threshold_identification,matrix-method threshold_identification-methods
Threshold indentification functionthreshold_identification_run
threshold_Results object and constructorthreshold_Results threshold_Results-class