Description Usage Arguments Value Examples
View source: R/sigfit_utility.R
retrieve_pars
obtains summary values for a set of model parameters (signatures, exposures,
activities or spectrum reconstructions) from a stanfit object.
1 | retrieve_pars(mcmc_samples, par, hpd_prob = 0.95)
|
mcmc_samples |
List with two elements named |
par |
Name of the parameter set to extract. Admits character values |
hpd_prob |
Numeric value in the interval (0, 1), indicating the desired probability content of HPD intervals (default is 0.95). |
A list of three matrices, which contain the values corresponding to the means of the model parameters and to the lower and upper ends of their HPD intervals, respectively.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | ## Not run:
# Load example mutational catalogues
data("counts_21breast")
# Extract signatures using the EMu (Poisson) model
samples <- extract_signatures(counts_21breast, nsignatures = 2, model = "emu",
opportunities = "human-genome", iter = 800)
# Retrieve signatures
signatures <- retrieve_pars(samples, "signatures")
# Retrieve exposures and activities using custom HPD intervals
exposures <- retrieve_pars(samples, "exposures", hpd_prob = 0.9)
activities <- retrieve_pars(samples, "activities", hpd_prob = 0.975)
# Retrieve reconstructed catalogues (reconstructions)
reconstructions <- retrieve_pars(samples, "reconstructions")
# Plot signatures, reconstructions and mean exposures
plot_spectrum(signatures)
plot_spectrum(reconstructions)
barplot(t(exposures$mean))
## End(Not run)
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