Add bin assignments to a strollur object

Usage

xdev_assign_bins(
  data,
  table,
  bin_type = "otu",
  reference = NULL,
  bin_name = "bin_name",
  abundance = "abundance",
  sample = "sample",
  sequence_name = "sequence_name",
  verbose = TRUE
)

Arguments

data: a strollur object
table: a data.frame containing bin_data 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'.
abundance: a string containing the name of the column in 'table' that contains the bin abundances. Default column name is 'abundance'. Note: You must provide either abundance or sequence_name in the table.
sample: a string containing the name of the column in 'table' that contains the sample names for datasets where the abundances are broken down by sample. Default column name is 'sample'.
sequence_name: a string containing the name of the column in 'table' that contains the sequence names. Default column name is 'sequence_name'. Note: You must provide either abundance or sequence_name in the table.
verbose: a boolean whether or not you want progress messages. Default = TRUE.

Value

an updated strollur object

Examples


  # To assign sequences to bins:

  data <- strollur::new_dataset(dataset_name = "miseq_sop")
  otu_data <- strollur::read_mothur_list(
                          list = strollur_example("final.opti_mcc.list.gz"))

  strollur::xdev_assign_bins(data, table = otu_data, bin_type = "otu")
#> Assigned 531 otu bins.
#> miseq_sop:
#> 
#> 
#> Number of unique seqs: 2425 
#> Total number of seqs: 2425 
#> 
#> Total number of otus: 531 
#> 

  # To add abundance only bin assignments:

  data <- strollur::new_dataset(dataset_name = "miseq_sop")
  otu_data <- strollur::read_mothur_rabund(
                         rabund = strollur_example("final.opti_mcc.rabund"))

  strollur::xdev_assign_bins(data, table = otu_data, bin_type = "otu")
#> Assigned 531 otu bins.
#> miseq_sop:
#> 
#> 
#> Number of unique seqs: 531 
#> Total number of seqs: 2425 
#> 
#> Total number of otus: 531 
#> 

  # To add abundance bin assignments parsed by sample:

  data <- strollur::new_dataset(dataset_name = "miseq_sop")
  otu_data <- readRDS(strollur_example("miseq_shared_otu.rds"))

  strollur::xdev_assign_bins(data, table = otu_data, bin_type = "otu")
#> Assigned 531 otu bins.
#> miseq_sop:
#> 
#> 
#> Number of unique seqs: 531 
#> Total number of seqs: 113963 
#> 
#> Total number of samples: 19 
#> Total number of otus: 531 
#>