prepareDatObject

generates BCdat object after barcode backbone identification.

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

prepareDatObject function

<dl><dt>dat</dt>
<dd>a tbl_df object (e.g. created by dplyr::count)</dd>
<dt>results_dir</dt>
<dd>a character string which contains the path to the results directory.</dd>
<dt>label</dt>
<dd>a character string which serves as a label for every kind of created output file.</dd>
<dt>bc_backbone</dt>
<dd>a character string describing the barcode design, variable positions have to be marked with the letter 'N'.</dd>
<dt>min_reads</dt>
<dd>positive integer value, all extracted barcode sequences with a read count smaller than min_reads will be excluded from the results</dd>
<dt>save_it</dt>
<dd>a logical value. If TRUE, the raw data will be saved as a csv-file.</dd></dl>

Arguments

Data Object Preparation — prepareDatObject

<dl>

<dt>dat</dt>
<dd>a tbl_df object (e.g. created by dplyr::count)</dd>


<dt>results_dir</dt>
<dd>a character string which contains the path to the results directory.</dd>


<dt>label</dt>
<dd>a character string which serves as a label for every kind of created output file.</dd>


<dt>bc_backbone</dt>
<dd>a character string describing the barcode design, variable positions have to be marked with the letter 'N'.</dd>


<dt>min_reads</dt>
<dd>positive integer value, all extracted barcode sequences with a read count smaller than min_reads will be excluded from the results</dd>


<dt>save_it</dt>
<dd>a logical value. If TRUE, the raw data will be saved as a csv-file.</dd>

</dl>

prepareDatObject: Data Object Preparation

Description

Usage

Value

Arguments