scGate (version 1.7.0)

combine_scGate_multiclass: Combine scGate annotations

Description

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"
)

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.

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

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")
query.seurat <- scGate(query.seurat, model=model.B,
    reduction="pca", output.col.name = "is.pure_Bcell")
query.seurat <- combine_scGate_multiclass(query.seurat, scGate_class=c("Tcell","Bcell"))      
table(query.seurat$scGate_multi)
# }