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

## Documentation for package ‘selectKSigs’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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