PrepInit: Initialize hdp object Allocate process index for hdp...

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

Initialize hdp object Allocate process index for hdp initialization. Prepare for hdp_init

Description

Initialize hdp object Allocate process index for hdp initialization. Prepare for hdp_init

Usage

PrepInit(
  multi.types,
  input.catalog,
  verbose = TRUE,
  K.guess,
  gamma.alpha = 1,
  gamma.beta = 1
)

Arguments

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.
input.catalog	Input spectra catalog as a matrix or in ICAMS format.
verbose	If TRUE then message progress information.
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.
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

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