Give true neighbors by level of prevalence

Usage

truth_by_prevalence(edge_table, prev_list)

Arguments

edge_table: Dataframe. The result of prev_for_selected_nodes()
prev_list: List of numeric. The prevalences to be studied. Required format is decimal: 0.20 for 20% of prevalence

Value

List of dataframes. Each element of the list corresponds to a dataframe of true edges by level of prevalence

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_truth <- prev_for_selected_nodes(tiny_data, tiny_graph, col_module_id = "msp_name", annotation_level = "species", object_of_interest = "bacterium")

tiny_true_edges <- truth_by_prevalence(tiny_truth, c(0.20, 0.30))
#> Defining and saving true neighbors...