Assign sequence abundance and optionally assign sample and treatment data to a strollur object
Usage
xdev_assign_sequence_abundance(
data,
table,
sequence_name = "sequence_name",
abundance = "abundance",
sample = "sample",
treatment = "treatment",
verbose = TRUE
)Arguments
- data,
a strollur object
- table,
a data.frame containing sequence abundance assignments
- sequence_name,
a string containing the name of the column in 'table' that contains the sequence names. Default column name is 'sequence_name'.
- abundance,
a string containing the name of the column in 'table' that contains the sequence abundances. Default column name is 'abundance'.
- sample,
a string containing the name of the column in 'table' that contains the sequence samples. Default column name is 'sample'. (Optional)
- treatment,
a string containing the name of the column in 'table' that contains the sequence treatments. Default column name is 'treatment'.
- verbose,
a boolean whether or not you want progress messages. Default = TRUE.
Value
an updated strollur object
Examples
data <- new_dataset("my_dataset")
sequence_abundance <- readRDS(strollur_example("miseq_abundance_by_sample.rds"))
xdev_assign_sequence_abundance(data = data, table = sequence_abundance)
#> Assigned 2425 sequence abundances.
#> my_dataset:
#>
#>
#> Number of unique seqs: 2425
#> Total number of seqs: 113963
#>
#> Total number of samples: 19
#> Total number of treatments: 2
#>