make_run_params: Helper function to package run parameters

In Wedge-Oxford/dpclust: DPClust - An R package for subclonal reconstruction of tumours using sequencing data

Helper function to package run parameters

Description

Helper function to package run parameters

Usage

make_run_params(no.iters, no.iters.burn.in, mut.assignment.type,
  num_muts_sample, is.male, min_muts_cluster = NULL,
  min_frac_muts_cluster = 0.01, species = "human",
  assign_sampled_muts = TRUE, supported_chroms = NULL,
  keep_temp_files = TRUE, generate_cluster_ordering = FALSE)

Arguments

no.iters	The number of iterations that the MCMC chain should be run for
no.iters.burn.in	The number of iterations that should be discarded as burn in of the MCMC chain
mut.assignment.type	Mutation assignment type option
num_muts_sample	The number of mutations from which to start downsampling
is.male	Boolean set to TRUE when the donor is male, female otherwise
min_muts_cluster	The minimum number of mutations required for a cluster to be kept in the final output (Default: NULL)
min_frac_muts_cluster	The minimum fraction of mutations required for a cluster to be kept in the final output (Default: 0.01)
species	Species (Default: Human)
assign_sampled_muts	A boolean whether to assign mutations that have not been used for clustering due to downsampling (Default: TRUE)
supported_chroms	Vector with chromosome names from which mutations can be used (Default: NULL)
keep_temp_files	Set to TRUE to keep temporary files (Default: TRUE)
generate_cluster_ordering	Set to TRUE to generate possible phylogenetic relationships between clusters (Default: FALSE)

Value

A list containing these components

Author(s)

sd11

Wedge-Oxford/dpclust documentation built on July 6, 2024, 2:02 p.m.