get_populations: SignIT population model without mutation signatures
In eyzhao/SignIT: What the Package Does (One Line, Title Case)

Description Usage Arguments Details Value

Inference of mutational subpopulations without joint inference of signatures

get_populations(
  mutation_table,
  n_populations,
  method = "mcmc",
  n_chains = 4,
  n_iter = 300,
  n_adapt = 200,
  n_cores = n_chains
)

`mutation_table`	Table of mutations, same as input to `get_population_signatures`.
`n_populations`	Number of populations to fit.
`method`	The method to use. Can be either "mcmc" for Hamiltonial Markov Chain Monte Carlo or "MAP" for maximum a posteriori estimate.
`n_chains`	Number of chains to use (only for `method == "mcmc"`)
`n_iter`	Number of sampling iterations per chain (only for `method == "mcmc"`)
`n_adapt`	Number of adaptation iterations per chain (only for `method == "mcmc"`)
`n_cores`	Number of cores for parallel sampling (by default equal to `n_chains`. only for `method == "mcmc"`)

This method can be used to obtain full posterior estimates of mutational subpopulations. It is also used under the hood by select_n_populations to perform automatic estimation of the number of populations for model selection.

List object with Stan output, parsed data, and relevant metadata

eyzhao/SignIT documentation built on Dec. 6, 2019, 11:45 a.m.