Data preprocessing 


MethylIT: Methylation Analysis Based on Signal Detection and Machine Learning 

Read files of methylation count tables 

Methylation pool from a list of GRanges objects with methylation read counts 

Information Divergences of Methylation Levels 

Signal detection 

Nonlinear fit of Information divergences distribution 

Report the Best Fitted Probability Distribution Model 

Potential methylation signal 

Selection of DMPs 

Estimate cutpoints to distinguish the treatment methylation signal from the control 

Evaluate DMPs Classification 

Differentially methylated regions 

Count DMPs at genebody 

Count DMPs at Genomic Regions 

Statistic of Genomic Regions 

DMP clustering 

Find Differentially Methylated Regions (DMRs) 

Data set constructor for class glmDataSet 

Regression Test for Count 

DMGs Estimation on Specified Genomic Region 

Base functions 

Unique genomic ranges from a list of GRanges objects 

Filter methylation counts by coverage in a GRanges object 

Information divergence estimator 

Select the beta distribution that fit specified quantiles 

Betabinomial Posterior Methylation Levels 

Hellinger divergence of methylation levels 

J Information Divergence of Methylation Levels 

Filter methylation counts by coverage 

Nonlinear fit of Generalized Gamma CDF (GGamma) 

Nonlinear fit of Gamma CDF (Gamma) 

Nonlinear fit of LogNormal CDF (LogNorm) 

Linear Discriminant Analysis (LDA) using Principal Component Analysis (PCA) 

Logistic Classification Model using Principal Component Analysis (PCA) 

Quadratic Discriminant Analysis (QDA) using Principal Component Analysis (PCA) 

Predict function for logistic regression model from 'LogisticR' class 

Predict DIMP class 

Sorting 'GRanges' objects 

Unique 

Auxiliary functions 

Boltzmann's Factors 

Extract Model Coefficients 

Fisher's exact test for read counts on GRanges objects 

Get Genes plus Up and Down Stream Regions 

Get Supplemental Files from GEO 

Generalized Gamma distribution 

Gibbs entropy of Generalized Gamma Distribution 

Helmholtz Free Energy of Generalized Gamma Distribution 

Molecular Machine Entropy 

Compute methylation levels 

Parallel Job Split 

Prediction Method of Random Forest for 'pDMP' Objects 

Predict function for probability distributions in MethylIT 

Weibull distribution with three parameters 

Generates intervals for a GRanges objects 

Nonlinear fit of Weibull CDF 

Data 

Simulated dataset of Hellinger divergences used in the examples 

Simulated dataset of Information divergences used in the examples 

Simulated dataset of potential DMPs used in examples 

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

Simulated dataset of DMPs used in examples 

Simulated dataset of RangedGlmDataSet class object (DMPs counts) 

Simulated dataset of nonlinear fits used in the examples 

Classification LDA model for simulated dataset of DMPs used in examples 

Classification logistic model for simulated dataset of DMPs used in examples 

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

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

Classification logistic model for simulated dataset of DMPs used in examples 

Classification LDA model for simulated dataset of DMPs used in examples 

Simulated dataset of read counts used in the examples 