Filter ASV abundance matrix and convert to taxmap and phyloseq objects

Usage

convert_asv_matrix_to_objs(
  analysis_setup,
  min_read_depth = 0,
  minimum_bootstrap = 0,
  save_outputs = FALSE
)

Arguments

analysis_setup: An object containing directory paths and data tables, produced by the prepare_reads function
min_read_depth: ASV filter parameter. If mean read depth of across all samples is less than this threshold, ASV will be filtered.
minimum_bootstrap: Set threshold for bootstrap support value for taxonomic assignments. Below designated minimum bootstrap threshold, taxnomoic assignments will be set to N/A
save_outputs: Logical, indicating whether to save the resulting phyloseq and taxmap objects. If TRUE, the objects will be saved; if FALSE, they will only be available in the global environment. Default is FALSE.

Value

ASV matrix converted to taxmap object

Examples

if (FALSE) { # \dontrun{
# Convert final matrix to taxmap and phyloseq objects for downstream analysis 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
)
assign_tax(
analysis_setup,
asv_abund_matrix,
retrieve_files=FALSE,
overwrite_existing=TRUE
)
objs<-convert_asv_matrix_to_objs(
analysis_setup
)
} # }