Package: selectKSigs 1.25.0

Zhi Yang

selectKSigs: Selecting the number of mutational signatures using a perplexity-based measure and cross-validation

A package to suggest the number of mutational signatures in a collection of somatic mutations using calculating the cross-validated perplexity score.

Authors:Zhi Yang [aut, cre], Yuichi Shiraishi [ctb]

# Install 'selectKSigs' in R:

install.packages('selectKSigs', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

c++– GNU Standard C++ Library v3
jags– Just Another Gibbs Sampler for Bayesian MCMC - binary JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS. JAGS was written with three aims in mind: * To have an engine for the BUGS language that runs on Unix * To be extensible, allowing users to write their own functions, distributions and samplers. * To be a plaftorm for experimentation with ideas in Bayesian modelling This package contains the 'jags' binary as well as the associated shared library modules loaded by the binary.

On BioConductor:selectKSigs-1.25.0(bioc 3.24)selectKSigs-1.24.0(bioc 3.23)

Last updated from:12a8f02471. Checks:1 WARNING, 13 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	247
linux-devel-arm64	OK	285
linux-devel-x86_64	OK	311
source / vignettes	OK	492
linux-release-arm64	OK	300
linux-release-x86_64	OK	592
macos-release-arm64	OK	205
macos-release-x86_64	OK	410
macos-oldrel-arm64	OK	247
macos-oldrel-x86_64	OK	491
windows-devel	OK	295
windows-release	OK	271
windows-oldrel	OK	257
wasm-release	OK	254

Last update: 2019-10-30
Started: 2019-09-16

Help page	Topics
A function for calculating the log-likelihood from the data and parameters	calcPMSLikelihood
Output the maximum potential scale reduction statistic of all parameters estimated	Calculate_Likelihood_test
Restore the converted parameter F for turboEM	convertFromTurbo_F
Restore the converted parameter Q for turboEM	convertFromTurbo_Q
Convert the parameter F so that turboEM can treat	convertToTurbo_F
Convert the parameter Q so that turboEM can treat	convertToTurbo_Q
Output the maximum potential scale reduction statistic of all parameters estimated	cv_PMSignature
Get the statsus of using the background signature	getBG
Get the count data in a matrix	getCounts
Get a matrix of mutational exposures of signatures	getExposures
Get a vector of possible features	getFeatures
Get a matrix of feature vector list	getFeatureVec
Get the number of signatures	getK
Get the values of loglikelihood	getLL
Calculate the value of the log-likelihood for given parameters	getLogLikelihoodC
Get the sample list	getSamplelist
Get the sample list	getSamplelistG
Get an array of signature feature distributions	getSignatures
Get the statsus of specifying the transcription bias	getTranscription
Output the training data or test data	select_kth_fold
Output the maximum potential scale reduction statistic of all parameters estimated	splitG