Calculate AUCell in Rust

The function will take in a list of gene set indices (0-indexed!) and calculate an AUCell type statistic. Two options here: calculate this with proper AUROC calculations (useful for marker gene expression) or based on the Mann-Whitney statistic (useful for pathway activity measurs). Data can be streamed in chunks of 50k cells per or loaded in in one go.

Usage

rs_aucell(f_path, gs_list, cells_to_keep, auc_type, streaming, verbose)

Arguments

f_path

String. Path to the counts_cells.bin file.

gs_list

List. List with the gene set indices (0-indexed!) of the genes of interest.

cells_to_keep

Integer. Vector of indices of the cells to keep.

auc_type

String. One of "wilcox" or "auroc", pending on which statistic you wish to calculate.

streaming

Boolean. Shall the data be streamed.

verbose

Boolean. Controls verbosity of the function.

Value

A matrix of cells x gene sets with the values representing the AUC.