Description Value See Also Examples
The multivariate HMM object is output of the function callPeaksMultivariate
and is a list()
with various entries. The class()
attribute of this list was set to "multiHMM". For a given hmm, the entries can be accessed with the list operators 'hmm[[]]' or 'hmm$'.
A list()
with the following entries:
info |
Experiment table for this object. |
bincounts |
A |
bins |
A |
segments |
Same as |
peaks |
A |
mapping |
A named vector giving the mapping from decimal combinatorial states to human readable combinations. |
weights |
Weight for each component. Same as |
weights.univariate |
Weights of the univariate HMMs. |
transitionProbs |
Matrix of transition probabilities from each state (row) into each state (column). |
transitionProbs.initial |
Initial |
startProbs |
Probabilities for the first bin. Same as |
startProbs.initial |
Initial |
distributions |
Emission distributions used for this model. |
convergenceInfo |
Contains information about the convergence of the Baum-Welch algorithm. |
convergenceInfo$eps |
Convergence threshold for the Baum-Welch. |
convergenceInfo$loglik |
Final loglikelihood after the last iteration. |
convergenceInfo$loglik.delta |
Change in loglikelihood after the last iteration (should be smaller than |
convergenceInfo$num.iterations |
Number of iterations that the Baum-Welch needed to converge to the desired |
convergenceInfo$time.sec |
Time in seconds that the Baum-Welch needed to converge to the desired |
correlation.matrix |
Correlation matrix of transformed reads. |
callPeaksMultivariate
, uniHMM
, combinedMultiHMM
1 2 3 4 | ## Get an example multiHMM
file <- system.file("data","multivariate_mode-combinatorial_condition-SHR.RData",
package="chromstaR")
model <- get(load(file))
|
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