dist_replacement,phyDat,missing,integer-method

Compute the kmer replacement distance between 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

dist_replacement,phyDat,missing,integer-method 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-mer length</dd>
<dt>...</dt>
<dd>other arguments passed to substr_kmer</dd></dl>

Arguments

Author

Compute the kmer replacement distance — dist_replacement,phyDat,missing,integer-method

<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-mer length</dd>


<dt>...</dt>
<dd>other arguments passed to substr_kmer</dd>

</dl>

dist_replacement,phyDat,missing,integer-method: Compute the kmer replacement distance

Description

Usage

Value

Arguments

Author