get_exposures: Compute the MCMC sample space of exposure vectors

In eyzhao/SignIT: What the Package Does (One Line, Title Case)

Description

At the heart of SignIT is the MCMC sampling of signature exposure solutions. This function provides a convenient wrapper around the MCMC sampling steps. It constructs the STAN model, runs it, and then returns the result in a well formatted list.

Usage

get_exposures(
  mutation_catalog,
  reference_signatures = NULL,
  priors = NULL,
  n_chains = 4,
  n_iter = 200,
  n_adapt = 200,
  n_cores = 1,
  stan_model = NULL,
  quiet = FALSE
)

Arguments

mutation_catalog	Data frame with columns mutation_type, count. The mutation types must be equivalent to those in reference_signatures.
reference_signatures	Reference mutation signatures, such as that output from get_reference_signatures.
n_chains	Number of MCMC chains
n_iter	Number of iterations per chain. Total iterations will be n_chains times n_iter.
n_adapt	Number of burn-in iterations

Value

List containing the MCMC samples, as well as other data such as reference signatures and mutation catalog.

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