If a single-cell dataset has precomputed results for multiple scGate models, combined them in multi-class annotation
Usage
combine_scGate_multiclass(
obj,
prefix = "is.pure_",
scGate_classes = NULL,
min_cells = 1,
multi.asNA = FALSE,
out_column = "scGate_multi"
)Arguments
- obj
Seurat object with scGate results for multiple models stored as metadata
- prefix
Prefix in metadata column names for scGate result models
- scGate_classes
Vector of scGate model names. If NULL, use all columns that start with "prefix" above.
- min_cells
Minimum number of cells for a cell label to be considered
- multi.asNA
How to label cells that are "Pure" for multiple annotations: "Multi" (FALSE) or NA (TRUE)
- out_column
The name of the metadata column where to store the multi-class cell labels
Value
A Seurat object with multi-class annotations based on the combination of multiple models. A new column (by default "scGate_multi") is added to the metadata of the Seurat object.
Examples
# \donttest{
# Define gating models
model.B <- gating_model(name = "Bcell", signature = c("MS4A1"))
model.T <- gating_model(name = "Tcell", signature = c("CD2","CD3D","CD3E"))
# Apply scGate with these models
data(query.seurat)
query.seurat <- scGate(query.seurat, model=model.T,
reduction="pca", output.col.name = "is.pure_Tcell")
#>
#> ### Detected a total of 71 pure 'Target' cells (23.67% of total)
query.seurat <- scGate(query.seurat, model=model.B,
reduction="pca", output.col.name = "is.pure_Bcell")
#>
#> ### Detected a total of 28 pure 'Target' cells (9.33% of total)
query.seurat <- combine_scGate_multiclass(query.seurat, scGate_class=c("Tcell","Bcell"))
table(query.seurat$scGate_multi)
#>
#> Bcell Tcell
#> 28 71
# }