OTU_taxonomy

Placeholder description for OTU_taxonomy dataset.

datasets

A series of R functions that come in handy while working with metabarcoding data.
The reasoning of doing this is to have the same functions we use all the time stored in a curated, reproducible way.
In a way it is all about putting together the grammar of the 'tidyverse' from Wickham et al.(2019) <doi:10.21105/joss.01686>
with the functions we have used in community ecology compiled in packages like 'vegan' from Dixon (2003) <doi:10.1111/j.1654-1103.2003.tb02228.x>
and 'phyloseq' McMurdie & Holmes (2013) <doi:10.1371/journal.pone.0061217>.
The package includes functions to read sequences from FAST(A/Q) into a tibble ('fasta_reader' and 'fastq_reader'),
to process 'cutadapt' Martin (2011) <doi:10.14806/ej.17.1.200> 'info-file' output. When it comes to sequence counts across samples, the package
works with the long format in mind (a three column 'tibble' with Sample, Sequence and counts ), with functions to move from there to the wider format.

Ramón Gallego Simón

eDNAfuns

Working with Metabarcoding Data in a Tidy Format

OTU_taxonomy function

A dataframe of DNA sequences names and their taxonomy, with 3 rows and 7 columns<dl>
 <dt>Hash</dt>
<dd>Sequence identifier</dd> <dt>Kingdom</dt>
<dd>taxon info at that rank</dd> <dt>Phylum</dt>
<dd>taxon info at that rank</dd> <dt>Class</dt>
<dd>taxon info at that rank</dd> <dt>Order</dt>
<dd>taxon info at that rank</dd> <dt>Family</dt>
<dd>taxon info at that rank</dd> <dt>Genus</dt>
<dd>taxon info at that rank</dd> 
</dl>

Format

OTU_taxonomy — OTU_taxonomy

A dataframe of DNA sequences names and their taxonomy, with 3 rows and 7 columns<dl>
 <dt>Hash</dt>
<dd>Sequence identifier</dd>

 <dt>Kingdom</dt>
<dd>taxon info at that rank</dd>

 <dt>Phylum</dt>
<dd>taxon info at that rank</dd>

 <dt>Class</dt>
<dd>taxon info at that rank</dd>

 <dt>Order</dt>
<dd>taxon info at that rank</dd>

 <dt>Family</dt>
<dd>taxon info at that rank</dd>

 <dt>Genus</dt>
<dd>taxon info at that rank</dd>

 
</dl>

OTU_taxonomy: OTU_taxonomy

Description

Usage

Arguments

Format