Assign bin classifications to a strollur object

Note, if you assign sequence taxonomies and assign bins, strollur 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_name",
  taxonomy = "taxonomy",
  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_name'.
taxonomy: a string containing the name of the column in 'table' that contains the bin taxonomies. Default column name is 'taxonomy'.
verbose: a boolean whether or not you want progress messages. Default = TRUE.

Value

an updated strollur object

Examples


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

data <- strollur::new_dataset(dataset_name = "my_dataset")

# assign otu abundances
strollur::xdev_assign_bins(data,
                             table = otu_data,
                             bin_type = "otu")
#> Assigned 531 otu bins.
#> my_dataset:
#> 
#> 
#> Number of unique seqs: 531 
#> Total number of seqs: 113963 
#> 
#> Total number of otus: 531 
#> 

# assign otu classifications
strollur::xdev_assign_bin_taxonomy(data,
                                     table = otu_data,
                                     bin_type = "otu")
#> Assigned 531 otu bin taxonomies.
#> my_dataset:
#> 
#> 
#> Number of unique seqs: 531 
#> Total number of seqs: 113963 
#> 
#> Total number of otus: 531 
#> Total number of otu bin classifications: 531 
#>