Assign sequence classifications to a strollur object

Assign sequence classifications to a strollur object

Note, if you assign sequence taxonomies and assign bins, strollur will find the consensus taxonomy for each bin for you.

Usage

xdev_assign_sequence_taxonomy(
  data,
  table,
  reference = NULL,
  sequence_name = "sequence_name",
  taxonomy = "taxonomy",
  verbose = TRUE
)

Arguments

data

a strollur object

table

a data.frame containing sequence taxonomy assignments

reference

a list created by the function new_reference. Optional.

sequence_name

a string containing the name of the column in 'table' that contains the sequence names. Default column name is 'sequence_name'.

taxonomy

a string containing the name of the column in 'table' that contains the sequence taxonomies. Default column name is 'taxonomy'.

verbose

a boolean whether or not you want progress messages. Default = TRUE.

Value

an updated strollur object

Examples

taxonomy <- strollur::read_mothur_taxonomy(strollur_example(
                        "final.taxonomy.gz"))

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

strollur::xdev_assign_sequence_taxonomy(data,
                                          table = taxonomy)
#> Assigned 2425 sequence taxonomies.
#> my_dataset:
#> 
#> 
#> Number of unique seqs: 2425 
#> Total number of seqs: 2425 
#> 
#> Total number of sequence classifications: 2425 
#> 

# With the reference parameter you can add information about the reference
# you used to classify your sequences. You can also add references using the
# 'strollur::xdev_add_references' function.

reference <- strollur::new_reference("trainset9_032012.pds.zip", "9_032012",
              "classification by mothur2 v1.0 using default options", "",
"https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset9_032012.pds.zip")

strollur::xdev_assign_sequence_taxonomy(data,
                                        table = taxonomy,
                                        reference = reference)
#> Assigned 2425 sequence taxonomies.
#> Added 1 resource references.
#> my_dataset:
#> 
#> 
#> Number of unique seqs: 2425 
#> Total number of seqs: 2425 
#> 
#> Total number of sequence classifications: 2425 
#> Total number of resource references: 1 
#>