summarize_kmer,phyDat-method

Summarize kmer distributions with input 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

summarize_kmer,phyDat-method function

<dl><dt>x</dt>
<dd>input data as a phyDat object</dd>
<dt>division</dt>
<dd>number of cell division</dd>
<dt>k</dt>
<dd>k-mer (default = 2)</dd>
<dt>reps</dt>
<dd>number of simulated trees</dd>
<dt>n_samples</dt>
<dd>number of samples to simulate</dd>
<dt>n_nodes</dt>
<dd>number of nodes to sample (including both leaves and internval nodes)</dd>
<dt>n_targets</dt>
<dd>sequence length. If this argument is missing, the length of the input sequences will be used.</dd></dl>

Arguments

Author

summarize_kmer — summarize_kmer,phyDat-method

<dl>

<dt>x</dt>
<dd>input data as a phyDat object</dd>


<dt>division</dt>
<dd>number of cell division</dd>


<dt>k</dt>
<dd>k-mer (default = 2)</dd>


<dt>reps</dt>
<dd>number of simulated trees</dd>


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


<dt>n_nodes</dt>
<dd>number of nodes to sample (including both leaves and internval nodes)</dd>


<dt>n_targets</dt>
<dd>sequence length. If this argument is missing, the length of the input sequences will be used.</dd>

</dl>

summarize_kmer,phyDat-method: summarize_kmer

Description

Usage

Value

Arguments

Author