gen_subj_truth: gen_subj_truth

In Sun-lab/SMASH: Subclone Multiplicity Allocation and Somatic Heterogeneity

gen_subj_truth

Description

Simulates copy number states, multiplicities, allocations

Usage

gen_subj_truth(mat_eS, maxLOCI, nCN = NULL)

Arguments

mat_eS	A subclone configuration matrix pre-defined in R list eS
maxLOCI	A positive integer number of simulated somatic variant calls
nCN	A positive integer for the number of allelic copy number pairings to sample from. If NULL, it will be randomly sampled between 1 and 5.

Value

A list containing the following components:

subj_truth

dataframe of each variant's simulated minor (CN_1) and major (CN_2) copy number states, total copy number (tCN), subclone allocation (true_A), multiplicity (true_M), mutant allele frequency (true_MAF), and cellular prevalence (true_CP)

purity

tumor purity

eta

the product of tumor purity and subclone proportions

q

vector of subclone proportions

Sun-lab/SMASH documentation built on March 5, 2025, 8 p.m.