bootPMSignature: Obtain the standard error estimates for parameters for...

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

Description

Obtain the standard error estimates for parameters for mutation signatures and memberships

Usage

bootPMSignature(mutationFeatureData, Param0, bootNum = 10, BG = NULL,
  tol = 0.01, maxIter = 10000)

Arguments

mutationFeatureData	the mutation data (MutationFeatureData class (S4 class)) by the readMPFile or readMFVFile functions.
Param0	the initial value for the parameter of memberships used for bootstrapped parameter estimations
bootNum	the number of bootstrapping
BG	the background signature used for estimating Param0
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

a list of standard error matrices (mutation signatures, membership parameters)

Examples

After obtaining mutationFeatureData (see e.g., by \code{readMPFile} function) as G, 
and EstimatedParameters (e.g., by \code{getPMSignature} function) as Param,
bootParam <- bootPMSignature(G, Param, bootNum = 100)

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