Extension to the package hdp for mutational signature discovery with the Hierarchical Dirichlet Process
Prior to installing hdpExtra, make sure that dependencies listed in the DESCRIPTION file are installed.
To install, use the devtools package
devtools::install_github("victorvelasco/hdpExtra")To infer mutational signatures, use the hdp package of Nicola Roberts to initialise an HDPM model
with the appropriate hierarchy of Dirichlet Process. To draw samples from the posterior distribution,
use our function hdpExtra::hdpExtra_posterior. This function has been adapted from hdp::hdp_posterior,
and saves the clustering allocations to memory so that it is possible to use our post-processing procedure.
Note that hdpExtra keeps full compatibility with hdp. Therefore, using hdp's post-processing procedure
with hdpExtra's output is also possible.
Our post-processing procedure allows one to find a representative solution of the vast MCMC output, and most importantly to quantify the uncertainty around that solution.