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 |
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]