FilterDisallowedClasses | R Documentation |
This is used to flag cells with high UCell score combinations generally indiciative of contamination or doublets
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"))
)
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. |
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