pmgetSignature {HiLDA} | R Documentation |
Obtain the parameters for mutation signatures and memberships
pmgetSignature(mutationFeatureData, K, numInit = 10, tol = 1e-04, maxIter = 10000)
mutationFeatureData |
the mutation data (MutationFeatureData class
(S4 class)) by the |
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 |
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
## After obtaining G (see e.g., hildaReadMPFile function) load(system.file("extdata/sample.rdata", package="HiLDA")) Param <- pmgetSignature(G, K = 3)