gen_subj_truth {SMASH}R Documentation

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


[Package SMASH version 1.0.0 Index]