make_asv_abund_matrix {demulticoder}R Documentation

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
)


[Package demulticoder version 0.1.2 Index]