xdev_set_abundances

Designed with package integration in mind, the set abundances function allows you to change the abundances of sequences in a strollur object with samples.

Usage

xdev_set_abundances(data, sequence_names, abundances, reason = "update")

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

No return value, called for side effects.

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_names = sequence_names,
                                             abundances = abundances,
                                             samples = samples))
#> Assigned 4 sequence abundances.
#> [1] 4

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)