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Helper function to generate HVG defaults

params_hvg_defaults.Rd

Helper function to generate HVG defaults

Usage

params_hvg_defaults()

Value

A named list with the following elements:

  • min_gene_var_pctl - Numeric. Which percentile of the highly variable genes to include. Defaults to 0.7.

  • hvg_method - String. Which method to use to identify HVG. One of c("vst", "mvb", "dispersion"). Defaults to "vst".

  • loess_span - Numeric. In case of "vst" the span of the loess function. Defaults to 0.3.

  • clip_max - Numeric or NULL. The maximum clipping value (optional). Defaults to NULL.

  • n_bins - Integer. The number of bins to use for the "mvb" HVG detection. Defaults to 20L.

  • binning_strategy - String. Which binning strategy to use for "mvb". One of c("equal_width", "equal_frequency"). Defaults to "equal_width".