Man pages for humburg/tileHMM
Hidden Markov Models for ChIP-on-Chip Analysis

baumWelchBaum-Welch Algorithm
contDist-classClass "contDist"
contHMM-accessAccessing Objects of Class "contHMM"
contHMM-classClass "contHMM"
discDist-classClass "discDist"
dist-accessAccessing and Converting Objects of Class "dist"
dist-classClass "dist"
forwardComputation of Forward and Backward Variables
generate.dataGenerate Simulated Dataset
getHMMCreate HMM from Parameter Values
gff2indexExtract Probe Calls from GFF File
hmm-classClass "hmm"
hmm.setupCreate HMM from Initial Parameter Estimates Obtained from...
initializeDist-methodsGenerating Objects of Class 'dist'
initializeHMM-methodsGenerate Objects of Class 'hmm'
internalsInternal Functions
logSumCalculate log(x + y) from log(x) and log(y)
plotPlotting of "contDist" Objects
posteriorCalculate Posterior Probability for States of HMM
reg2gffConverting Information about Enriched Regions into GFF Format
region.lengthDetermine Length of Positive and Negative Regions
region.positionIdentify Enriched Regions
remove.shortPost-Processing of "tileHMM" Results
sampleObsSample Observations from Probability Distribution
sampleSeqGenerate Observation Sequence from HMM
shrinkt.stCalculate 'Shrinkage t' Statistic
simChIPSimulated ChIP-on-Chip Data
statesState Names of Hidden Markov Model
tDist-classClass "tDist"
tileHMM-packageHidden Markov Models for ChIP-on-Chip Analysis
viterbiCalculate Most Likely State Sequence Using the Viterbi...
viterbiEMEfficient Estimation of HMM Parameters
viterbiTrainingEstimate HMM Parameters Using Viterbi Training
humburg/tileHMM documentation built on May 17, 2019, 9:13 p.m.