A	packageHelpers
A,betaHMMResults-method	packageHelpers
A,NULL-method	packageHelpers
A,RangedSummarizedExperiment-method	packageHelpers
annotatedData	packageHelpers
annotatedData,betaHMMResults-method	packageHelpers
annotatedData,threshold_Results-method	packageHelpers
annotation_data	annotation_data
AUC	packageHelpers
AUC,dmcResults-method	packageHelpers
AUC,NULL-method	packageHelpers
AUC,RangedSummarizedExperiment-method	packageHelpers
AUC_DM_analysis	AUC_DM_analysis
backward	backward
BaumWelch	BaumWelch
betaHMM	betaHMM
betaHMM,data.frame,data.frame-method	betaHMM
betaHMM,data.frame,GRanges-method	betaHMM
betaHMM,data.frame,matrix-method	betaHMM
betaHMM,data.frame,RangedSummarizedExperiment-method	betaHMM
betaHMM,data.frame,RangedSummarizedExperiment.-method	betaHMM
betaHMM,GRanges,data.frame-method	betaHMM
betaHMM,GRanges,GRanges-method	betaHMM
betaHMM,GRanges,matrix-method	betaHMM
betaHMM,GRanges,RangedSummarizedExperiment-method	betaHMM
betaHMM,matrix,data.frame-method	betaHMM
betaHMM,matrix,GRanges-method	betaHMM
betaHMM,matrix,matrix-method	betaHMM
betaHMM,matrix,RangedSummarizedExperiment-method	betaHMM
betaHMM,matrix,RangedSummarizedExperiment.-method	betaHMM
betaHMM,RangedSummarizedExperiment,data.frame-method	betaHMM
betaHMM,RangedSummarizedExperiment,GRanges-method	betaHMM
betaHMM,RangedSummarizedExperiment,matrix-method	betaHMM
betaHMM,RangedSummarizedExperiment,RangedSummarizedExperiment-method	betaHMM
betaHMM,RangedSummarizedExperiment,RangedSummarizedExperiment.-method	betaHMM
betaHMM-methods	betaHMM
betaHMMResults	betaHMMResults
betaHMMResults-class	betaHMMResults
betaHMMrun	betaHMMrun
chromosome_number	packageHelpers
chromosome_number,betaHMMResults-method	packageHelpers
chromosome_number,dmrResults-method	packageHelpers
chromosome_number,NULL-method	packageHelpers
chromosome_number,RangedSummarizedExperiment-method	packageHelpers
dmcResults	dmcResults
dmcResults-class	dmcResults
dmc_identification	dmc_identification
dmc_identification,betaHMMResults-method	dmc_identification
dmc_identification-methods	dmc_identification
dmc_identification_run	dmc_identification_run
dmrResults	dmrResults
dmrResults-class	dmrResults
dmr_identification	dmr_identification
dmr_identification,data.frame-method	dmr_identification
dmr_identification,dmcResults-method	dmr_identification
dmr_identification,matrix-method	dmr_identification
dmr_identification-methods	dmr_identification
dmr_identification_run	dmr_identification_run
forward	forward
hidden_states	packageHelpers
hidden_states,betaHMMResults-method	packageHelpers
hidden_states,NULL-method	packageHelpers
hidden_states,RangedSummarizedExperiment-method	packageHelpers
hidden_states,threshold_Results-method	packageHelpers
initialise_parameters	initialise_parameters
K	packageHelpers
K,betaHMMResults-method	packageHelpers
K,dmcResults-method	packageHelpers
K,NULL-method	packageHelpers
K,RangedSummarizedExperiment-method	packageHelpers
K,threshold_Results-method	packageHelpers
llk	packageHelpers
llk,betaHMMResults-method	packageHelpers
llk,NULL-method	packageHelpers
llk,RangedSummarizedExperiment-method	packageHelpers
model_parameters	packageHelpers
model_parameters,NULL-method	packageHelpers
model_parameters,RangedSummarizedExperiment-method	packageHelpers
model_parameters,threshold_Results-method	packageHelpers
N	packageHelpers
N,betaHMMResults-method	packageHelpers
N,dmcResults-method	packageHelpers
N,NULL-method	packageHelpers
N,RangedSummarizedExperiment-method	packageHelpers
pca_methylation_data	pca_methylation_data
phi	packageHelpers
phi,betaHMMResults-method	packageHelpers
phi,NULL-method	packageHelpers
phi,RangedSummarizedExperiment-method	packageHelpers
phi,threshold_Results-method	packageHelpers
plot	plot
plot,betaHMMResults-method	plot
plot,dmcResults-method	plot
plot,threshold_Results-method	plot
plot-methods	plot
R	packageHelpers
R,betaHMMResults-method	packageHelpers
R,dmcResults-method	packageHelpers
R,NULL-method	packageHelpers
R,RangedSummarizedExperiment-method	packageHelpers
sample_annotation_file	sample_annotation_file
sample_methylation_file	sample_methylation_file
summary	summary
summary,betaHMMResults-method	summary
summary,dmcResults-method	summary
summary,dmrResults-method	summary
summary-methods	summary
tau	packageHelpers
tau,betaHMMResults-method	packageHelpers
tau,NULL-method	packageHelpers
tau,RangedSummarizedExperiment-method	packageHelpers
threshold	packageHelpers
threshold,NULL-method	packageHelpers
threshold,RangedSummarizedExperiment-method	packageHelpers
threshold,threshold_Results-method	packageHelpers
threshold_identification	threshold_identification
threshold_identification,data.frame-method	threshold_identification
threshold_identification,matrix-method	threshold_identification
threshold_identification-methods	threshold_identification
threshold_identification_run	threshold_identification_run
threshold_Results	threshold_Results
threshold_Results-class	threshold_Results
treatment_group	packageHelpers
treatment_group,betaHMMResults-method	packageHelpers
treatment_group,dmcResults-method	packageHelpers
treatment_group,NULL-method	packageHelpers
treatment_group,RangedSummarizedExperiment-method	packageHelpers
uncertainty	packageHelpers
uncertainty,dmcResults-method	packageHelpers
uncertainty,NULL-method	packageHelpers
uncertainty,RangedSummarizedExperiment-method	packageHelpers
Viterbi	Viterbi
