Data preprocessing

MethylIT

MethylIT: Methylation Analysis Based on Signal Detection and Machine Learning

readCounts2GRangesList()

Read files of methylation count tables

poolFromGRlist()

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

estimateDivergence()

Information Divergences of Methylation Levels

Signal detection

nonlinearFitDist()

Nonlinear fit of Information divergences distribution

gofReport()

Report the Best Fitted Probability Distribution Model

getPotentialDIMP()

Potential methylation signal

selectDIMP()

Selection of DMPs

estimateCutPoint()

Estimate cutpoints to distinguish the treatment methylation signal from the control

evaluateDIMPclass()

Evaluate DMPs Classification

Differentially methylated regions

getDIMPatGenes()

Count DMPs at gene-body

getDMPatRegions()

Count DMPs at Genomic Regions

dmpClusters()

DMP clustering

glmDataSet()

Data set constructor for class glmDataSet

countTest2()

Regression Test for Count

Base functions

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 Log-Normal 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

Auxiliary functions

FisherTest()

Fisher's exact test for read counts on GRanges objects

getGEOSuppFiles()

Get Supplemental Files from GEO

dggamma() pggamma() qggamma() rggamma()

Generalized Gamma distribution

pweibull3P()

Weibull distribution with three parameters

weibull3P()

Nonlinear fit of Weibull CDF

Data

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