convert_asv_matrix_to_objs {demulticoder}R Documentation

Filter ASV abundance matrix and convert to 'taxmap' and 'phyloseq' objects

Description

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, taxonomic 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


# 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(),
  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
)


[Package demulticoder version 0.1.2 Index]