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.

Value

The ASV abundance matrix (asv_abund_matrix)

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.

Examples

if (FALSE) { # \dontrun{
# The primary wrapper function for DADA2 ASV inference steps
analysis_setup <- prepare_reads(
  data_directory = system.file("extdata", package = "demulticoder"),
  output_directory = tempdir(),
  tempdir_path = tempdir(),
  tempdir_id = "demulticoder_run_temp",
  overwrite_existing = TRUE
)
cut_trim(
analysis_setup,
cutadapt_path="/usr/bin/cutadapt",
overwrite_existing = TRUE
)
make_asv_abund_matrix(
analysis_setup,
overwrite_existing = TRUE
)
} # }