dist_kmer_replacement_inference

Compute the sequence distance matrix using inferred kmer replacement matrix

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

dist_kmer_replacement_inference function

<dl><dt>x</dt>
<dd>input data in phyDat format</dd>
<dt>kmer_summary</dt>
<dd>a kmer_summary object</dd>
<dt>k</dt>
<dd>k-mers (default k=2)</dd></dl>

Arguments

Author

Core function of computing kmer replacement distance — dist_kmer_replacement_inference

<dl>

<dt>x</dt>
<dd>input data in phyDat format</dd>


<dt>kmer_summary</dt>
<dd>a kmer_summary object</dd>


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

</dl>

dist_kmer_replacement_inference: Core function of computing kmer replacement distance

Description

Usage

Value

Arguments

Author