pmgetSignature: Obtain the parameters for mutation signatures and memberships

Description Usage Arguments Value Examples

View source: R/pm_getSignature.R

Description

Obtain the parameters for mutation signatures and memberships

Usage

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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

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

HiLDA documentation built on Nov. 8, 2020, 11:09 p.m.