ASV_table

An abundance table in long format.

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

ASV_table function

A data frame with 9 rows and 3 variables:<dl>
 <dt>sample_name</dt>
<dd>Character vector, last digit includes PCR replicate</dd> <dt>Hash</dt>
<dd>The sequence found, hashed using sha1 for consistency</dd> <dt>nReads</dt>
<dd>Number of times that hash was found in that sample</dd>
</dl>

Format

ASV_table — ASV_table

A data frame with 9 rows and 3 variables:<dl>
 <dt>sample_name</dt>
<dd>Character vector, last digit includes PCR replicate</dd>

 <dt>Hash</dt>
<dd>The sequence found, hashed using sha1 for consistency</dd>

 <dt>nReads</dt>
<dd>Number of times that hash was found in that sample</dd>


</dl>

ASV_table: ASV_table

Description

Usage

Arguments

Format

Details