Designed with package integration in mind, the set abundances function allows you to change the abundances of sequences in a strollur object with samples.
Arguments
- data,
a strollur object
- sequence_names,
a vector of strings containing sequence names
- abundances,
2D vector ([num_seqs][num_samples]) containing the abundances of each sequence parsed by sample.
- reason,
a string containing the trash tag to be applied to any sequences set to 0 abundance. Default = "update".
Value
an updated strollur object
Examples
data <- new_dataset(dataset_name = "my_dataset")
sequence_names <- c("seq1", "seq1", "seq1", "seq2", "seq2", "seq2", "seq3",
"seq3", "seq4")
samples <- c("sample2", "sample3", "sample4", "sample2", "sample3",
"sample4", "sample2", "sample3", "sample4")
abundances <- c(250, 400, 500, 25, 40, 50, 25, 25, 4)
xdev_assign_sequence_abundance(data = data,
table = data.frame(sequence_name = sequence_names,
abundance = abundances,
sample = samples))
#> Assigned 4 sequence abundances.
#> my_dataset:
#>
#>
#> Number of unique seqs: 4
#> Total number of seqs: 1319
#>
#> Total number of samples: 3
#>
seqs_to_update <- c("seq4")
new_abunds <- list(c(20, 10, 4))
xdev_set_abundances(data = data,
sequence_names = seqs_to_update,
abundances = new_abunds)
#> my_dataset:
#>
#>
#> Number of unique seqs: 4
#> Total number of seqs: 1349
#>
#> Total number of samples: 3
#>