marker_ranking_boruta {HDStIM} | R Documentation |
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 |
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)
attribute_stats <- marker_ranking_boruta(mapped_data, path = NULL, n_cells = NULL,
max_runs = 1000, seed_val = 123,
verbose = 0)
[Package HDStIM version 0.1.0 Index]