assign_taxa: Assign Taxa

In aquaMetrics/aquaman: Assess Size of the Mixing Zone

Assign Taxa

Description

WORK IN PROGRESS - DO NOT USE IN PRODUCTION - based on dada2 tutorial https://benjjneb.github.io/dada2/tutorial.html. Assign family taxa from .fastq files. Will prompt you to download taxonomic reference file on first use or user can provide ‘taxonomy_file = ’...'' path.

Usage

assign_taxa(
  path = NULL,
  folder_pattern = NULL,
  taxonomy_file = NULL,
  tax_level = NULL,
  multithread = FALSE,
  save_output = FALSE
)

Arguments

path	to folder containing folder(s) of fastq files. Assumes .fastq files have format ‘SAMPLENAME_XXXX.fastq' - XXXX... Must Be ’L001_R1_001' or L001_R2_001' as per normal Illumina naming. SAMPLENAME Must Be unique at least within the path.
folder_pattern	Optional Character string to match against folders to analyse. Often "001" can be used to identify Illumina generated folders.
taxonomy_file	Optional path to taxonomy file e.g. ...silva_nr99_v138.1_train_set.fa.gz, otherwise will try to download file.
tax_level	The taxonomic levels being assigned. Default is "Family", options are c("Kingdom", "Phylum", "Class", "Order", "Family", "genus", "Species").
multithread	Set to FALSE on windows. Only applies to dada2::filterAndTrim function 'https://github.com/benjjneb/dada2/issues/1100'. The rest of the DADA2 functions will use multithread even on windows.
save_output	Boolean to indicating if taxa assigment data is saved/appended to 'output.csv' should be saved in the path after each folder. This can save progress if errors or crashes happen before completion.

Value

dataframe containing assigned fmaily level taxa

Examples

## Not run: 
taxa <- assign_taxa(path = demo_path())

## End(Not run)

aquaMetrics/aquaman documentation built on June 14, 2025, 7:48 a.m.