Description Usage Arguments Value Author(s) References Examples
This function fits a three-state HMM with mixture model of Zero-Inflated Negative Binomials for differential peak detection across conditions with replicates.
1 | mixZINBHMM(object, control)
|
object |
a mixNBHMMDataSet |
control |
list of control arguments from controlEM() |
The mixNBHMMDataSet with the following list as metadata
:
Vector of estimated initial probabilities of the HMM
Vector of estimated transition probabilities of the HMM
Vector of estimated means and dispersion parameters pertaining to the emission distributions
Data table of window-based (rows) posterior probabilities of the HMM emission distributions (columns)
Data table of window-based (rows) posterior probabilities of the mixture model from each mixture component (columns)
Vector of Viterbi sequence of hidden states
Data table of window-based (rows) log forward probabilities from the emission distributions (columns)
Data table of window-based (rows) log backward probabilities from the emission distributions (columns)
Data table of window-based (rows) log probabilities from the emission distributions (columns)
Data table of parameter estimates (column) from every EM iteration (rows)
IMPORTANT: the output mixNBHMMDataSet has conditions and replicates reordered. Make sure to check colData()
of your output.
Pedro L. Baldoni, pedrobaldoni@gmail.com
https://github.com/plbaldoni/mixNBHMM
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