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Calculate the percentage of gene sets in the cells

rs_sc_hvg.Rd

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

Usage

rs_sc_hvg(
  f_path_gene,
  hvg_method,
  cell_indices,
  loess_span,
  clip_max,
  streaming,
  verbose
)

Arguments

f_path_gene

String. Path to the counts_genes.bin file.

hvg_method

String. Which HVG detection method to use. Options are c("vst", "meanvarbin", "dispersion"). So far, only the first is implemented.

cell_indices

Integer positions (0-indexed!) that defines the cells to keep.

loess_span

Numeric. The span parameter for the loess function.

clip_max

Optional clipping number. Defaults to sqrt(no_cells) if not provided.

streaming

Boolean. Shall the genes be streamed in to reduce memory pressure.

verbose

Boolean. Controls verbosity of the function.

Value

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

  • mean - The average expression of the gene.

  • var - The variance of the gene.

  • var_exp - The expected variance of the gene.

  • var_std - The standardised variance of the gene.