ScAnnotator: Automatic annotation of cell types

In WubingZhang/scAnalyzer: Integrative analysis pipeline for analyzing single-cell RNA-seq data

Automatic annotation of cell types

Description

Automatic annotation of cell types

Usage

scAnnotator(
  query.obj,
  group.by = "seurat_clusters",
  method = c("seurat"),
  ref.data = NULL,
  ref.ann = NULL,
  markers = NULL,
  plot = TRUE,
  outdir = "./"
)

Arguments

query.obj	A seurat object for cell type annotation.
group.by	A character specifying the cluster column in meta.data.
method	A vector specifying the cell type annotation methods. Should be one of singler, sclearn, scmap-cell, scmap-cluster, seurat
ref.data	A matrix like object specifying the reference data or a Seurat object.
ref.ann	A vector specifying the cell type annotation of the reference data.
markers	A list with Positive (markers$Positive) and Negative markers (markers$Negative) of cell types.
plot	A boolean indicating whether to save and visualize the prediction results.
outdir	Path to the output directory.

Value

A seurat object with prediction results added into meta.data.

Author(s)

Wubing Zhang

WubingZhang/scAnalyzer documentation built on Jan. 30, 2023, 10:11 p.m.