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_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 <- 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.
#> my_dataset:
#>
#>
#> Number of unique seqs: 531
#> Total number of seqs: 113963
#>
#> Total number of otus: 531
#>
# assign otu classifications
xdev_assign_bin_taxonomy(data = 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
#>