SCENIC on MetaCells — rs_mc_scenic • bixverse

Assumes that the sparse data is pre-filtered for the cells and genes you wish to include: every column is a target gene. The regressors read the second layer, which here is an f32 cast of the supplied counts.

Usage

rs_mc_scenic(sparse_data, tf_indices, scenic_params, seed, verbose)

Arguments

sparse_data: A named list that needs to have data, indptr, indices, nrow, ncol and cs_type. Shape is (metacells, genes).
tf_indices: Integer vector. 0-indexed(!) column positions of the transcription factors within sparse_data.
scenic_params: Named list. Contains all of the parameters needed for SCENIC, see params_scenic().
seed: Integer. Controls reproducibility of the function.
verbose: Integer. 0L - quiet; 1L - normal verbosity; 2L - detailed verbosity.

Value

A genes x TFs importance matrix, rows in column order of sparse_data, columns in the order of tf_indices.