.HMM

HMM-class


This class is a generic container for Hidden Markov Models.


STAN (STrand-specic ANnotation of genomic data) implements
bidirectional Hidden Markov Models (bdHMM), which are designed
for studying directed genomic processes, such as gene
transcription, DNA replication, recombination or DNA repair by
integrating genomic data. bdHMMs model a sequence of successive
observations (e.g. ChIP or RNA measurements along the genome)
by a discrete number of 'directed genomic states', which e.g.
reflect distinct genome-associated complexes. Unlike standard
HMM approaches, bdHMMs allow the integration of strand-specific
(e.g. RNA) and non strand-specific data (e.g. ChIP).

Benedikt Zacher

STAN

STrand-specific ANnotation of genomic data

HMM-class function

 <dl>
<dt><code>initProb</code></dt><dd>Initial state probabilities.</dd> <dt><code>transMat</code></dt><dd>Transition probabilities</dd> <dt><code>emission</code></dt><dd>Emission parameters as an HMMEmission object.</dd> <dt><code>nStates</code></dt><dd>Number of states.</dd> <dt><code>status</code></dt><dd>of the HMM. On of c('initial', 'EM').</dd> </dl>

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HMM-class: This class is a generic container for Hidden Markov Models.

Description

Arguments

Slots

See Also

Examples