xdev_assign_bin_representative_sequences

Assign representative sequences to bins.

Usage

xdev_assign_bin_representative_sequences(
  data,
  table,
  bin_type = "otu",
  reference = NULL,
  bin_name = "bin_names",
  sequence_name = "sequence_names",
  verbose = TRUE
)

Arguments

data,

a strollur object

table,

a data.frame containing bin representative 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_names'.

sequence_name

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

verbose,

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

Value

double containing the number of representative sequences assigned

Examples

  miseq <- miseq_sop_example()
#> Added 2425 sequences.
#> Assigned 2425 sequence abundances.
#> Assigned 2425 sequence taxonomies.
#> Assigned 531 otu bins.
#> Assigned 2425 asv bins.
#> Assigned 63 phylotype bins.
#> Assigned 19 samples to treatments.
#> Assigned 531 otu bin taxonomies.
#> Assigned 531 otu bin representative sequences.
#> Added metadata.
#> Added 2 resource references.
#> Added a contigs_report.

  bin_reps <- readRDS(strollur_example(
         "miseq_representative_sequences.rds"))

  xdev_assign_bin_representative_sequences(data = miseq,
                                      table = bin_reps,
                                      bin_type = "otu")
#> Assigned 531 otu bin representative sequences.
#> [1] 531