.getMinDist

Calculates the minimum distance to a set of predefined barcodes for a given list of barcode.

Provides the necessary functions to identify and extract a selection of already available barcode constructs (Cornils, K. et al. (2014) <doi:10.1093/nar/gku081>) and freely choosable barcode designs from next generation sequence (NGS) data. Furthermore, it offers the possibility to account for sequence errors, the calculation of barcode similarities and provides a variety of visualisation tools (Thielecke, L. et al. (2017) <doi:10.1038/srep43249>).

Lars Thielecke

genBaRcode

Analysis and Visualization Tools for Genetic Barcode Data

.getMinDist function

<dl><dt>BC_dat</dt>
<dd>a BCdat object</dd>
<dt>ori_BCs</dt>
<dd>a character vector containing barcodes to which the minimal hamming distance will be calculated.</dd>
<dt>m</dt>
<dd>a character string, Method for distance calculation, default value is Hamming distance. Possible values
are "osa", "lv", "dl", "hamming", "lcs", "qgram", "cosine", "jaccard", "jw", "soundex" (see stringdist function
of the stringdist-package for more information).</dd></dl>

Arguments

Distance calculation — .getMinDist

<dl>

<dt>BC_dat</dt>
<dd>a BCdat object</dd>


<dt>ori_BCs</dt>
<dd>a character vector containing barcodes to which the minimal hamming distance will be calculated.</dd>


<dt>m</dt>
<dd>a character string, Method for distance calculation, default value is Hamming distance. Possible values
are "osa", "lv", "dl", "hamming", "lcs", "qgram", "cosine", "jaccard", "jw", "soundex" (see stringdist function
of the stringdist-package for more information).</dd>

</dl>

.getMinDist: Distance calculation

Description

Usage

Arguments