Filter genes for SCENIC GRN inference — scenic_gene_filter

Filters genes by minimum total counts and minimum expressed-cell fraction using the SCENIC inclusion criteria. Returns a character vector of gene identifiers passing both filters.

Usage

scenic_gene_filter_sc(
  object,
  scenic_params = params_scenic(),
  cells_to_take = NULL,
  .verbose = TRUE
)

Arguments

object: SingleCells class.
scenic_params: List. SCENIC parameters, see params_scenic(). Only min_counts and min_cells are used by this function.
cells_to_take: Optional string vector. Cell identifiers to restrict to. If NULL, defaults to all filtered cells in the class.
.verbose: Boolean. Controls verbosity. Defaults to TRUE.

Value

A character vector of gene identifiers passing the SCENIC inclusion criteria.