runCellClassify: runCellClassify

In wguo-research/scCancer: A package for automated processing of single cell RNA-seq data in cancer

runCellClassify

Description

Use a one-class logistic regression (OCLR) model to predict cancer microenvironment cell types.

Usage

runCellClassify(
  expr,
  cell.annotation,
  coor.names = c("tSNE_1", "tSNE_2"),
  savePath,
  ct.templates = NULL,
  species = "human"
)

Arguments

expr	A Seurat object.
cell.annotation	A data.frame of cells' annotation.
coor.names	A vector indicating the names of two-dimension coordinate used in visualization.
savePath	A path to save the results files. If NULL, the 'statPath' will be used instead.
ct.templates	A list of vectors of several cell type templates. The default is NULL and the templates prepared in this package will be used.
species	A character string indicating what species the sample belong to. Only "human"(default) or "mouse" are allowed.

Value

A list of updated Seurat object, cell.annotation, and the plots for cell type annotation.

wguo-research/scCancer documentation built on May 26, 2024, 9:12 p.m.