getAvgSignal

A list containing the viterbi paths as factors. The output from getViterbi.

viterbi

The observations. A list of one or more entries containing the observation matrix (<code>numeric</code>) for the samples (e.g. chromosomes).


Compute average signal in state segmentation


Genome segmentation with hidden Markov models has become a useful tool to annotate genomic elements, such as promoters and enhancers. STAN (genomic STate ANnotation) implements (bidirectional) hidden Markov models (HMMs) using a variety of different probability distributions, which can model a wide range of current genomic data (e.g. continuous, discrete, binary). STAN de novo learns and annotates the genome into a given number of 'genomic states'. The 'genomic states' may for instance reflect distinct genome-associated protein complexes (e.g. 'transcription states') or describe recurring patterns of chromatin features (referred to as 'chromatin states'). Unlike other tools, STAN also allows for the integration of strand-specific (e.g. RNA)  and non-strand-specific data (e.g. ChIP).

getAvgSignal: Compute average signal in state segmentation

Description

Usage

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Examples