xdev_assign_sequence_taxonomy

Assign sequence classifications to a strollur object

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

Usage

xdev_assign_sequence_taxonomy(
  data,
  table,
  reference = NULL,
  sequence_name = "sequence_names",
  taxonomy = "taxonomies",
  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_names'.

taxonomy,

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

verbose,

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

Value

double containing the number of sequence assigned

Examples

sequence_classifications <- read_mothur_taxonomy(strollur_example(
                        "final.taxonomy.gz"))

data <- new_dataset("my_dataset", 2)

xdev_assign_sequence_taxonomy(data, sequence_classifications)
#> Assigned 2425 sequence taxonomies.
#> [1] 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
# 'add_references' function.

reference <- 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")

xdev_assign_sequence_taxonomy(data, sequence_classifications, reference)
#> Assigned 2425 sequence taxonomies.
#> [1] 2425