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Identify HVGs

find_hvg_sc.Rd

This is a helper function to identify highly variable genes. At the moment the implementation has only the VST-based version (known as Seurat v3). The other methods will be implemented in the future.

Usage

find_hvg_sc(
  object,
  hvg_no = 2000L,
  hvg_params = params_sc_hvg(),
  streaming = FALSE,
  .verbose = TRUE
)

Arguments

object

SingleCells class.

hvg_no

Integer. Number of highly variable genes to include. Defaults to 2000L.

hvg_params

List, see params_sc_hvg(). This list contains

  • method - Which method to use. One of c("vst", "meanvarbin", "dispersion")

  • loess_span - The span for the loess function to standardise the variance

  • num_bin - Integer. Not yet implemented.

  • bin_method - String. One of c("equal_width", "equal_freq"). Not implemented yet.

streaming

Boolean. Shall the genes be streamed in. Useful for larger data sets where you wish to avoid loading in the whole data. Defaults to FALSE.

.verbose

Boolean. Controls verbosity and returns run times.

Value

It will add the mean, var, var_exp, var_std of each gene to the the var table.