marker_ranking_boruta: Marker Ranking by Boruta

In niaid/HDStIM: High Dimensional Stimulation Immune Mapping ('HDStIM')

Marker Ranking by Boruta

Description

Function to run Boruta on the stimulation - cell population combinations that passed the Fisher's exact test to rank the markers according to their contribution to the response.

Usage

marker_ranking_boruta(
  mapped_data,
  path = NULL,
  n_cells = NULL,
  max_runs = 100,
  seed_val = 123,
  verbose = 0
)

Arguments

mapped_data	Returned list from the HDStIM function.
path	Path to the folder to save figures generated by this function.
n_cells	Number of cells to down sample the data. Default is NULL to include all the cells.
max_runs	Maximum number of runs for the random forest algorithm. Default is 100.
seed_val	Seed value for Boruta. Default is 123.
verbose	0, 1, or 2. Default is 0.

Value

A list with a tibble containing attribute statistics calculated by Boruta and ggplot objects. If the path is not NULL, plots are also rendered and saved in the specified folder in PNG format.

Examples

mapped_data <- HDStIM(chi11$expr_data, chi11$state_markers,
                      chi11$cluster_col, chi11$stim_label,
                      chi11$unstim_label, seed_val = 123, umap = FALSE, umap_cells = NULL,
                      verbose = FALSE)

marker_ranking <- marker_ranking_boruta(mapped_data, path = NULL, n_cells = NULL,
                                        max_runs = 1000, seed_val = 123,
                                        verbose = 0)

niaid/HDStIM documentation built on Oct. 15, 2023, 4:43 p.m.