as.data.frame.discDist
                        Accessing and Converting Objects of Class
                        "dist"
baumWelch               Baum-Welch Algorithm
contDist-class          Class "contDist"
contHMM-access          Accessing Objects of Class "contHMM"
contHMM-class           Class "contHMM"
discDist-class          Class "discDist"
dist-class              Class "dist"
forward                 Computation of Forward and Backward Variables
generate.data           Generate Simulated Dataset
getHMM                  Create HMM from Parameter Values
gff2index               Extract Probe Calls from GFF File
hmm-class               Class "hmm"
hmm.setup               Create HMM from Initial Parameter Estimates
                        Obtained from Data
initialize,contDist-method
                        Generating Objects of Class 'dist'
initialize,contHMM-method
                        Generate Objects of Class 'hmm'
logSum                  Calculate log(x + y) from log(x) and log(y)
plot                    Plotting of "contDist" Objects
posterior               Calculate Posterior Probability for States of
                        HMM
reg2gff                 Converting Information about Enriched Regions
                        into GFF Format
region.length           Determine Length of Positive and Negative
                        Regions
region.position         Identify Enriched Regions
remove.short            Post-Processing of "tileHMM" Results
sampleObs               Sample Observations from Probability
                        Distribution
sampleSeq               Generate Observation Sequence from HMM
shrinkt.st              Calculate 'Shrinkage t' Statistic
simChIP                 Simulated ChIP-on-Chip Data
states                  State Names of Hidden Markov Model
tDist-class             Class "tDist"
tileHMM-package         Hidden Markov Models for ChIP-on-Chip Analysis
viterbi                 Calculate Most Likely State Sequence Using the
                        Viterbi Algorithm
viterbiEM               Efficient Estimation of HMM Parameters
viterbiTraining         Estimate HMM Parameters Using Viterbi Training
