simulate,lineage_tree_config,phyDat-method

Simulate a cell lineage tree based on a set of sequences

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,lineage_tree_config,phyDat-method function

<dl><dt>config</dt>
<dd>simulation configuration; a lineage_tree_config object</dd>
<dt>x</dt>
<dd>a sequence object</dd>
<dt>n_samples</dt>
<dd>number of samples to simulate</dd>
<dt>k</dt>
<dd>Number of trials</dd>
<dt>greedy</dt>
<dd>Whether ot not use a greedy search</dd>
<dt>...</dt>
<dd>additional parameters</dd></dl>

Arguments

Author

simulate — simulate,lineage_tree_config,phyDat-method

<dl>

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


<dt>x</dt>
<dd>a sequence object</dd>


<dt>n_samples</dt>
<dd>number of samples to simulate</dd>


<dt>k</dt>
<dd>Number of trials</dd>


<dt>greedy</dt>
<dd>Whether ot not use a greedy search</dd>


<dt>...</dt>
<dd>additional parameters</dd>

</dl>

simulate,lineage_tree_config,phyDat-method: simulate

Description

Usage

Value

Arguments

Author