List the simulated count tables by level of prevalence

Usage

simulate_by_prevalence(
  data_with_annotation,
  prev_list,
  graph_file = NULL,
  col_module_id,
  annotation_level,
  sample_size = 500,
  seed,
  verbatim = FALSE,
  data_type = "shotgun"
)

Arguments

data_with_annotation: Dataframe. The abundance table merged with the module names. Required format: modules are the rows and samples are the columns. The first column must be the modules name (e.g. species), the second is the module ID (e.g. msp), and each subsequent column is a sample
prev_list: List of numeric. The prevalences to be studied. Required format is decimal: 0.20 for 20% of prevalence.
graph_file: Dataframe. The object generated by graph_step() function
col_module_id: String. The name of the column with the module names in data_with_annotation
annotation_level: String. The name of the column with the level to be studied. Examples: species, genus, level_1
sample_size: Numeric. The size to be considerated, the value of 500 is recommended
seed: Numeric. The seed number, ensuring reproducibility
verbatim: Boolean. Controls verbosity
data_type: String. Enables the treatment of 16S data with "16S", default value is "shotgun"

Value

List of dataframes. Each element of the list corresponds to a level of prevalence and is a simulated abundance table

Examples

tiny_data <- data.frame(
  species = c("One bacteria", "One bacterium L", "One bacterium G", "Two bact"),
  msp_name = c("msp_1", "msp_2", "msp_3", "msp_4"),
  SAMPLE1 = c(0, 1.328425e-06, 0, 1.527688e-07),
  SAMPLE2 = c(1.251707e-07, 1.251707e-07, 3.985320e-07, 0),
  SAMPLE3 = c(0, 0, 4.926046e-09, 5.626392e-06),
  SAMPLE4 = c(0, 0, 2.98320e-05, 0)
)

tiny_graph <- graph_step(tiny_data, col_module_id = "msp_name", annotation_level = "species", seed = 20242025) %>% suppressWarnings()

tiny_sims <- simulate_by_prevalence(tiny_data, prev_list = c(0.20, 0.30), graph_file = tiny_graph, col_module_id = "msp_name", annotation_level = "species", sample_size = 500, seed = 20242025)