Man pages for steverozen/mSigHdp
Mutational signature discovery using HDP (hierarchical Dirichlet process)
| Burnin | Run the Gibbs sampling burnin (one thread) |
| CleanChlist | If the job of Gibbs sampling from 'ParallelGibbsSamble' has... |
| CombineChainsAndExtractSigs | Extract signatures etc. from multiple Gibbs sample chains |
| ComponentDiagnosticPlotting | Generate diagnostic plots from the return value of... |
| downsample | Downsample a vector of type 'numeric'; nonsensical for... |
| downsample_spectra | Downsample a set of mutational spectra |
| ExtendBurnin | Extend burnin iterations generated from 'Burnin' |
| GenerateAverageCluster | Generate average pattern of clusters of each posterior chain... |
| Generateppindex | Generate index for a HDP structure and num.tumor.types for... |
| GeneratePriorppindex | Generate index for a HDP structure and num.tumor.types for... |
| GibbsSamplingAfterBurnin | Start Gibbs sampling on one chain after burnin |
| ParallelGibbsSample | Setup hierarchical Dirichlet processes and run parallel Gibbs... |
| PlotSamplesHighSigExp | Plot hdp signature exposure in each sample. This function... |
| PrepInit | Initialize hdp object Allocate process index for hdp... |
| RunHdpxParallel | Extract (discover) mutational signatures from a matrix of... |
| SaveAnalysis | Save the analysis from 'CombineChainsAndExtractSigs' to... |
| SetupAndActivate | Generate an HDP Gibbs sampling chain from a spectra catalog. |
| SetupAndPosterior | Generate an HDP Gibbs sampling chain from a spectra catalog |
| show_downsample_curves | Show the effects of the downsample_threshold argument to... |
