RecoverUnassignedCells — RecoverUnassignedCells • RIRA

This step recovers unassigned cells by inspecting each cluster and assigning Unassigned cells to the match the cluster majority

Usage

RecoverUnassignedCells(
  seuratObj,
  classField = "RIRA_Immune_v2.cellclass",
  groupField = "ClusterNames_0.2",
  targetField = "RIRA_Immune_v2.cellclass.recovered",
  unassignedValues = c("Unassigned", "Unknown"),
  minClusterProp = 0.6
)

Arguments

seuratObj: The seurat object
classField: The name of the field holding the cell type call
groupField: The field on which to group, such as the cluster ID
targetField: The field that will store the result
unassignedValues: A list of string values that denote Unassigned/Unknown cells
minClusterProp: If at least this proportion of the group is one class, unassigned cells will be assigned as this class

Value

The updated seurat object