Select markers for SPOTlight using an `screference`

Select markers for SPOTlight using an `screference`

Usage

spotlight_scref(
  scref,
  n_hvg = 3000,
  marker_selection_method = "mean.AUC",
  marker_selection_params = list(min = 0.8, max = Inf),
  downsample_n_cells = 100
)

Arguments

scref

an `screference` object

n_hvg

number of highly variable genes to be evaluated

marker_selection_method

a string with the name of a metric, indicating how to select markers. See `scran::scoreMarkers` for available metrics.

marker_selection_params

a list of parameters to select marker genes. `min` and `max` are currently supported. For example, for `marker_selection_method = "mean.AUC"`, `min = 0.8` indicates markers have minimum mean AUC of 0.8, while `max = Inf` indicates no maximum value of mean AUC.

downsample_n_cells

an integer, how many cells of each type to keep in the reference

Value

reference results to be used for SPOTlight deconvolution.