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_tidy(
data,
table,
reference = NULL,
sequence_name = "sequence_names",
level = "levels",
taxonomy = "taxonomies",
confidence = "confidences",
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'.
- level,
a string containing the name of the column in 'table' that contains the taxonomy levels. Default column name is 'levels'.
- taxonomy,
a string containing the name of the column in 'table' that contains the sequence taxonomies. Default column name is 'taxonomies'.
- confidence,
a string containing the name of the column in 'table' that contains the taxonomies confidence. Default column name is 'confidences'.
- verbose,
a boolean whether or not you want progress messages. Default = TRUE.
Examples
sequence_classifications <- readRDS(strollur_example("miseq_tidy_taxonomy.rds"))
data <- new_dataset("my_dataset")
xdev_assign_sequence_taxonomy_tidy(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_tidy(data, sequence_classifications, reference)
#> Assigned 2425 sequence taxonomies.
#> [1] 2425