pmgetSignature: Obtain the parameters for mutation signatures and memberships

In USCbiostats/HiLDA: Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation

Description

Obtain the parameters for mutation signatures and memberships

Usage

pmgetSignature(
  mutationFeatureData,
  K,
  numInit = 10,
  tol = 1e-04,
  maxIter = 10000
)

Arguments

mutationFeatureData	the mutation data (MutationFeatureData class (S4 class)) by the hildaReadMPFile.
K	the number of mutation signatures
numInit	the number of performing calculations with different initial values
tol	tolerance for the estimation (when the difference of log-likelihoods become below this value, stop the estimation)
maxIter	the maximum number of iteration of estimation

Value

The output is an instance of EstimatedParameters S4 class, which stores estimated parameters and other meta-information, and will be used for saving parameter values and visualizing the mutation signatures and memberships

Examples

## After obtaining G (see e.g., hildaReadMPFile function)
load(system.file("extdata/sample.rdata", package="HiLDA"))
Param <- pmgetSignature(G, K = 3)

USCbiostats/HiLDA documentation built on Oct. 15, 2021, 10:22 a.m.