Run hitype_assign for a Seurat object

Usage

RunHitype(object, ...)

# S3 method for default
RunHitype(object, ...)

# S3 method for Seurat
RunHitype(
  object,
  gs = NULL,
  fallback = "Unknown",
  threshold = 0.05,
  level_weights = function(l) 1/(10^(l - 1)),
  make_unique = FALSE,
  slot = "data",
  assay = NULL,
  scaled = FALSE,
  ...
)

Arguments

object: Seurat object
gs: The gene list prepared by gs_prepare
fallback: A fallback cell type if no cell type is assigned
threshold: A threshold for low confidence cell type assignment The cell types are only assigned for cells with scores higher than the threshold. (0 - 1, default 0.05)
level_weights: The weights for each level of the hierarchy to calculate the final cell type score It should be either a numeric vector of length equal to the number of levels or a single numeric value to be used for all levels It can also be a function that takes the levels as input and returns a numeric vectors as the weights.
make_unique: Whether to make the cell type names unique
slot: The slot to use for GetAssayData
assay: The assay to use for GetAssayData
scaled: Whether the data from GetAssayData is scaled

Value

The Seurat object with the cell types (named hitype) added to the metadata