Package: betaHMM 1.1.0

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]

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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'))

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-1.1.0(bioc 3.20)betaHMM-1.0.0(bioc 3.19)

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

bioconductor-package

29 exports 1.00 score 69 dependencies

Last updated 2 months agofrom:047a0a30b5

Exports:A annotatedData AUC betaHMM betaHMMResults betaHMMrun chromosome_number dmc_identification dmc_identification_run dmcResults dmr_identification dmr_identification_run dmrResults hidden_states K llk model_parameters N phi plot R summary tau threshold threshold_identification threshold_identification_run threshold_Results treatment_group uncertainty

Dependencies:abind askpass Biobase BiocGenerics cli codetools colorspace cowplot cpp11 crayon curl DelayedArray doParallel dplyr fansi farver foreach generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable httr IRanges isoband iterators jsonlite labeling lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pillar pkgconfig plyr pROC purrr R6 RColorBrewer Rcpp rlang S4Arrays S4Vectors scales SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

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 Jun 30 2024.

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

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

Package: betaHMM 1.1.0

betaHMM: A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Beta-Valued DNA Methylation Data

betaHMM package: Quick-start guide

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)