# Hidden Markov Models for ChIP-on-Chip Analysis

## Documentation for package ‘tileHMM’ version 1.0-7

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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
show-method | Class "contDist"
show-method | Class "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"