uniqueGRanges()

Unique genomic ranges from a list of GRanges objects 
filterGRange()

Filter methylation counts by coverage in a GRanges object 
estimateBayesianDivergence()

Information divergence estimator 
estimateHellingerDiv()

Hellinger divergence of methylation levels 
estimateJDiv()

J Information Divergence of Methylation Levels 
filterByCoverage()

Filter methylation counts by coverage 
fitGGammaDist()

Nonlinear fit of Generalized Gamma CDF (GGamma) 
fitGammaDist()

Nonlinear fit of Gamma CDF (Gamma) 
fitLogNormDist()

Nonlinear fit of LogNormal CDF (LogNorm) 
pcaLDA() predict(<pcaLDA>)

Linear Discriminant Analysis (LDA) using Principal Component Analysis
(PCA) 
pcaLogisticR() predict(<pcaLogisticR>)

Logistic Classification Model using Principal Component
Analysis (PCA) 
pcaQDA() predict(<pcaQDA>)

Quadratic Discriminant Analysis (QDA) using Principal Component
Analysis (PCA) 
predict(<LogisticR>)

Predict function for logistic regression model from 'LogisticR' class 
predictDIMPclass()

Predict DIMP class 
sortBySeqnameAndStart() sortBySeqnameAndEnd()

Sorting 'GRanges' objects 
uniqueGRfilterByCov()

Unique GRanges of methylation read counts filtered by coverages 
HD

Simulated dataset of Hellinger divergences used in the examples 
PS

Simulated dataset of potential DMPs used in examples 
cutpoint

Cutpoint of the 'PS' simulated dataset used in the examples 
dmps

Simulated dataset of DMPs used in examples 
ds

Simulated dataset of RangedGlmDataSet class object (DMPs counts) 
gof

Simulated dataset of nonlinear fits used in the examples 
lda_perf

Classification LDA model for simulated dataset of DMPs used in examples 
logit_perf

Classification logistic model for simulated dataset of DMPs used in examples 
pcaLda_perf

Classification PCA+LDA model for simulated dataset of DMPs used in examples 
pcaQda_perf

Classification PCA+QDA model for simulated dataset of DMPs used in examples 
pcalogit_perf

Classification logistic model for simulated dataset of DMPs used in examples 
qda_perf

Classification LDA model for simulated dataset of DMPs used in examples 