SetupAndActivate: Generate an HDP Gibbs sampling chain from a spectra catalog.

In steverozen/mSigHdp: Mutational signature discovery using HDP (hierarchical Dirichlet process)

Generate an HDP Gibbs sampling chain from a spectra catalog.

Description

Generate an HDP Gibbs sampling chain from a spectra catalog.

Usage

SetupAndActivate(
  input.catalog,
  seedNumber = 1,
  K.guess,
  multi.types = FALSE,
  verbose = TRUE,
  gamma.alpha = 1,
  gamma.beta = 20
)

Arguments

input.catalog	Input spectra catalog as a matrix or in ICAMS format.
seedNumber	A random seed that ensures ensures reproducible results.
K.guess	Suggested initial value of the number of raw clusters. Usually, the number of raw clusters is roughly twice the number of extracted signatures. Passed to hdpx::dp_activate as argument initcc.
multi.types	A logical scalar or a character vector. If FALSE, The HDP analysis will regard all input spectra as one tumor type, and the HDP structure will have one parent node for all tumors. If TRUE, Sample IDs in input.catalog must have the form sample_type::sample_id. If a character vector, then its length must be ncol(input.catalog), and each value is the sample type of the corresponding column in input.catalog, e.g. c(rep("Type-A", 23), rep("Type-B", 10)) for 23 Type-A samples and 10 Type-B samples. If not FALSE, HDP will have one parent node for each sample type and one grandparent node.
verbose	If TRUE then message progress information.
gamma.alpha	Shape parameter of the gamma distribution prior for the Dirichlet process concentration parameters α_0 and all α_j in Figure B.1 of https://www.repository.cam.ac.uk/bitstream/handle/1810/275454/Roberts-2018-PhD.pdf
gamma.beta	Inverse scale parameter (rate parameter) of the gamma distribution prior for the Dirichlet process concentration parameters: β_0 and all β_j in Figure B.1 of https://www.repository.cam.ac.uk/bitstream/handle/1810/275454/Roberts-2018-PhD.pdf We recommend gamma.alpha = 1 and gamma.beta = 20 for single-base-substitution signature extraction; gamma.alpha = 1 and gamma.beta = 50 for doublet-base-substitution and indel signature extraction

Value

Invisibly, an hdpState-class object as returned from dp_activate.

steverozen/mSigHdp documentation built on Feb. 6, 2023, 1:36 a.m.