Calculate the percentage of gene sets in the cells — rs_sc_get_gene_set_perc • bixverse

This function allows to calculate for example the proportion of mitochondrial genes, or ribosomal genes in the cells for QC purposes.

Usage

rs_sc_get_gene_set_perc(
  f_path_cell,
  gene_set_idx,
  cell_indices,
  streaming,
  verbose
)

Arguments

f_path_cell: String. Path to the counts_cells.bin file.
gene_set_idx: Named list with integer(!) positions (0-indexed!) as elements of the genes of interest.
cell_indices: Integer. The indices of the cells for which to calculate the proportions. (0-indexed!)
streaming: Boolean. Shall the data be worked on in chunks.
verbose: Boolean. Controls verbosity of the function.

Value

A list with the percentages of counts per gene set group detected in the cells.