Hidden Markov Models for ChIP-on-Chip Analysis


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Documentation for package ‘tileHMM’ version 1.0-3

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tileHMM-package Hidden Markov Models for ChIP-on-Chip Analysis
as.data.frame.discDist Accessing and Converting Objects of Class "dist"
as.matrix.discDist Accessing and Converting Objects of Class "dist"
as.vector.discDist Accessing and Converting Objects of Class "dist"
backward Computation of Forward and Backward Variables
backward-method Computation of Forward and Backward Variables
baumWelch Baum-Welch Algorithm
baumWelch-method 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
forward-method 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,contHMM Class "contHMM"
initialize-method Generating Objects of Class 'dist'
initialize-method Generate Objects of Class 'hmm'
length-method Accessing Objects of Class "contHMM"
length-method Accessing and Converting Objects of Class "dist"
logSum Calculate log(x + y) from log(x) and log(y)
new-method Generating Objects of Class 'dist'
new-method Generate Objects of Class 'hmm'
plot Plotting of "contDist" Objects
plot.contDist Plotting of "contDist" Objects
plot.contHMM Plotting of "contDist" Objects
plot.tDist 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
sampleObs-method Sample Observations from Probability Distribution
sampleSeq Generate Observation Sequence from HMM
sampleSeq-method Generate Observation Sequence from HMM
shrinkt.st Calculate 'Shrinkage t' Statistic
simChIP Simulated ChIP-on-Chip Data
states State Names of Hidden Markov Model
states-method State Names of Hidden Markov Model
tDist-class Class "tDist"
tileHMM Hidden Markov Models for ChIP-on-Chip Analysis
viterbi Calculate Most Likely State Sequence Using the Viterbi Algorithm
viterbi-method Calculate Most Likely State Sequence Using the Viterbi Algorithm
viterbiEM Efficient Estimation of HMM Parameters
viterbiTraining Estimate HMM Parameters Using Viterbi Training
viterbiTraining-method Estimate HMM Parameters Using Viterbi Training
[.contDist Accessing and Converting Objects of Class "dist"
[.contHMM Accessing Objects of Class "contHMM"
[.discDist Accessing and Converting Objects of Class "dist"
[.tDist Accessing and Converting Objects of Class "dist"
[<-.contDist Accessing and Converting Objects of Class "dist"
[<-.tDist Accessing and Converting Objects of Class "dist"
[[.discDist Accessing and Converting Objects of Class "dist"