make_asv_abund_matrix: Make an amplified sequence variant (ASV) abundance matrix for...

In demulticoder: Simultaneous Analysis of Multiplexed Metabarcodes

Make an amplified sequence variant (ASV) abundance matrix for each of the input barcodes

Description

Make an amplified sequence variant (ASV) abundance matrix for each of the input barcodes

Usage

make_asv_abund_matrix(analysis_setup, overwrite_existing = FALSE)

Arguments

analysis_setup	An object containing directory paths and data tables, produced by the prepare_reads function
overwrite_existing	Logical, indicating whether to overwrite existing results. Default is FALSE.

Details

The function processes data for each unique barcode separately, inferring ASVs, merging reads, and creating an ASV abundance matrix. To do this, the 'DADA2' core denoising alogrithm is used to infer ASVs.

Value

The ASV abundance matrix (asv_abund_matrix)

Examples

# The primary wrapper function for 'DADA2' ASV inference steps
analysis_setup <- prepare_reads(
  data_directory = system.file("extdata", package = "demulticoder"),
  output_directory = tempdir(),
  overwrite_existing = TRUE
)
cut_trim(
analysis_setup,
cutadapt_path="/usr/bin/cutadapt",
overwrite_existing = TRUE
)
make_asv_abund_matrix(
analysis_setup,
overwrite_existing = TRUE
)

demulticoder documentation built on June 8, 2025, 12:47 p.m.