Filter Disallowed Classes

This is used to flag cells with high UCell score combinations generally indiciative of contamination or doublets

Usage

FilterDisallowedClasses(
  seuratObj,
  sourceField = "RIRA_Immune_v2.majority_voting",
  outputFieldName = "DisallowedUCellCombinations",
  ucellCutoff = 0.2,
  disallowedClasses = list(T_NK = c("Bcell.RM_UCell", "Myeloid.RM_UCell",
    "Erythrocyte.RM_UCell", "Platelet.RM_UCell", "NeutrophilLineage.RM_UCell"), Myeloid =
    c("Bcell.RM_UCell", "Tcell.RM_UCell", "NK.RM_UCell", "Erythrocyte.RM_UCell",
    "Platelet.RM_UCell"), Bcell = c("Tcell.RM_UCell", "NK.RM_UCell", "Myeloid.RM_UCell",
    "Erythrocyte.RM_UCell", "Platelet.RM_UCell", "NeutrophilLineage.RM_UCell",
    "Complement.RM_UCell"))
)

Arguments

seuratObj

The seurat object

sourceField

The name of the field on which to compare

outputFieldName

The name of the field to store the results

ucellCutoff

Any cells expressing the disallowed UCell above this value will be flagged

disallowedClasses

This is a list where the names are the cell classes (which should match levels in sourceField), and values are a vector of UCell field names.