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xdev_assign_bins

Source: R/RcppExports.R
xdev_assign_bins.Rd

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

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

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

  xdev_assign_bins(data = 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 
#>