combine_scGate_multiclass: Combine scGate annotations

In scGate: Marker-Based Cell Type Purification for Single-Cell Sequencing Data

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"
)

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

# 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)

scGate documentation built on May 29, 2024, 2:56 a.m.