xdev_assign_bin_taxonomy — xdev_assign_bin

Assign bin classifications to a strollur object

Note, if you assign sequence taxonomies and assign bins, 'Dataset' will find the concensus taxonomy for each bin for you.

Usage

xdev_assign_bin_taxonomy(
  data,
  table,
  bin_type = "otu",
  reference = NULL,
  bin_name = "bin_names",
  taxonomy = "taxonomies",
  verbose = TRUE
)

Arguments

data,: a strollur object
table,: a data.frame containing bin taxonomy assignments
bin_type: a string indicating the type of bin assignments. Default "otu".
reference,: a list created by the function [new_reference]. Optional.
bin_name,: a string containing the name of the column in 'table' that contains the bin names. Default column name is 'bin_names'.
taxonomy,: a string containing the name of the column in 'table' that contains the bin taxonomies. Default column name is 'taxonomies'.
verbose,: a boolean whether or not you want progress messages. Default = TRUE.

Value

double containing the number of bins assigned

Examples


otu_data <- read_mothur_cons_taxonomy(strollur_example(
                        "final.cons.taxonomy"))

data <- new_dataset(dataset_name = "my_dataset")

# assign otu abundances
xdev_assign_bins(data = data, table = otu_data, bin_type = "otu")
#> Assigned 531 otu bins.
#> [1] 531

# assign otu classifications
xdev_assign_bin_taxonomy(data = data, table = otu_data,
                         bin_type = "otu")
#> Assigned 531 otu bin taxonomies.
#> [1] 531