gen_subj_truth

Simulates copy number states, multiplicities, allocations

Cluster user-supplied somatic read counts with corresponding allele-specific copy number and tumor purity to infer feasible underlying intra-tumor heterogeneity in terms of number of subclones, multiplicity, and allocation (Little et al. (2019) <doi:10.1186/s13073-019-0643-9>).

Paul Little

SMASH

Subclone Multiplicity Allocation and Somatic Heterogeneity

gen_subj_truth function

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

Arguments

gen_subj_truth — gen_subj_truth

<dl>

<dt>mat_eS</dt>
<dd>A subclone configuration matrix pre-defined in R list <code>eS</code></dd>


<dt>maxLOCI</dt>
<dd>A positive integer number of simulated somatic variant calls</dd>


<dt>nCN</dt>
<dd>A positive integer for the number of allelic copy number pairings 
to sample from. If <code>NULL</code>, it will be randomly sampled between 1 and 5.</dd>

</dl>

gen_subj_truth: gen_subj_truth

Description

Usage

Value

Arguments