Hidden Markov Models for ChIP-on-Chip Analysis

baumWelch | Baum-Welch Algorithm |

contDist-class | Class "contDist" |

contHMM-access | Accessing Objects of Class "contHMM" |

contHMM-class | Class "contHMM" |

discDist-class | Class "discDist" |

dist-access | Accessing and Converting Objects of Class "dist" |

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... |

initializeDist-methods | Generating Objects of Class 'dist' |

initializeHMM-methods | Generate Objects of Class 'hmm' |

internals | Internal Functions |

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... |

viterbiEM | Efficient Estimation of HMM Parameters |

viterbiTraining | Estimate HMM Parameters Using Viterbi Training |

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