simulate_core

Simulate a cell lineage tree
Adoped from https://github.com/elifesciences-publications/CRISPR_recorders_sims/blob/master/MATLAB_sims/GESTALT_30hr_1x_simulation.m

R codes for distance based cell lineage reconstruction. Our methods won both sub-challenges 2 and 3 of the Allen Institute Cell Lineage Reconstruction DREAM Challenge in 2020.
References: Gong et al. (2021) <doi:10.1016/j.cels.2021.05.008>, Gong et al. (2022) <doi:10.1186/s12859-022-04633-x>.

Il-Youp Kwak

DCLEAR

Distance Based Cell Lineage Reconstruction

Wuming Gong

simulate_core function

<dl><dt>config</dt>
<dd>simulation configuration; a lineage_tree_config object</dd>
<dt>tree</dt>
<dd>a matrix representing the lineage tree</dd>
<dt>mutation_site</dt>
<dd>a binary matrix indicating the mutation sites</dd>
<dt>outcome</dt>
<dd>a character matrix</dd></dl>

Arguments

simulate_core — simulate_core

<dl>

<dt>config</dt>
<dd>simulation configuration; a lineage_tree_config object</dd>


<dt>tree</dt>
<dd>a matrix representing the lineage tree</dd>


<dt>mutation_site</dt>
<dd>a binary matrix indicating the mutation sites</dd>


<dt>outcome</dt>
<dd>a character matrix</dd>

</dl>

simulate_core: simulate_core

Description

Usage

Value

Arguments