getPMSignature: Obtain the parameters for mutation signatures and memberships

In friend1ws/pmsignature: Extracting characteristic mutation signatures from a set of mutation data.

Description

Obtain the parameters for mutation signatures and memberships

Usage

getPMSignature(mutationFeatureData, K, BG = NULL, numInit = 10,
  tol = 1e-04, maxIter = 10000)

Arguments

mutationFeatureData	the mutation data (MutationFeatureData class (S4 class)) by the readMPFile or readMFVFile functions.
K	the number of mutation signatures
BG	a background mutation features typically provided by readBGFile function (default: NULL)
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 mutationFeatureData (see e.g., readMPFile function) as G,
Param <- getPMSignature(G, K = 3)

When using background signature
BG_prob <- readBGFile(G)
Param <- getPMSignature(G, K = 3, BG = BG_prob)

friend1ws/pmsignature documentation built on May 16, 2019, 3:27 p.m.