getAvgSignal: Compute average signal in state segmentation
In STAN: The Genomic STate ANnotation Package

Description Usage Arguments Value Examples

Compute average signal in state segmentation

1	getAvgSignal(viterbi, obs, fct=mean)

`viterbi`	A list containing the viterbi paths as factors. The output from getViterbi.
`obs`	The observations. A list of one or more entries containing the observation matrix (`numeric`) for the samples (e.g. chromosomes).
`fct`	The averaging function, default: mean.

A state x data track matrix containing the average signal.

data(yeastTF_databychrom_ex)
dStates = 6
dirobs = as.integer(c(rep(0,10), 1, 1))
bdhmm_gauss = initBdHMM(yeastTF_databychrom_ex, dStates = dStates, method = "Gaussian", directedObs=dirobs)
bdhmm_fitted_gauss = fitHMM(yeastTF_databychrom_ex, bdhmm_gauss)
viterbi_bdhmm_gauss = getViterbi(bdhmm_fitted_gauss, yeastTF_databychrom_ex)
avg_signal = getAvgSignal(viterbi_bdhmm_gauss, yeastTF_databychrom_ex)