Identify_CellType: Identify cell type of each cluster

In CACIMAR: Cross-Species Analysis of Cell Identities, Markers and Regulations

Identify cell type of each cluster

Description

This function has three steps to identify cell type of each cluster. (1) Calculate the power of each known marker based on AUC (area under the receiver operating characteristic curve of gene expression) which indicates the capability of marker i from cell type m to distinguish cluster j and the other clusters. (2) Calculate the united power (UP) for cell type m across each cluster j. (3) For each cluster j we determine the cell type according to UP. Generally, the cluster beongs to the cell type which have the highest united power or higher than the threshold of the united power (for example > 0.9 power).

Usage

Identify_CellType(seurat_object, Marker_gene_table)

Arguments

seurat_object	seurat object
Marker_gene_table	data.frame, indicating marker gene and its corresponding cell type. Marker_gene_table should contain two columns: 'CellType' represent correseponding cell types of each marker and 'Marker' represent Markers

Value

Cell type with the highest power in each cluster

Examples

KnownMarker=data.frame(c('AIF1','BID','CCL5','CD79A','CD79B','MS4A6A'),c('a','a','a','b','b','b'))
data("pbmc_small")
colnames(KnownMarker)=c('Marker','CellType')
CT <- Identify_CellType(pbmc_small,KnownMarker)

CACIMAR documentation built on May 18, 2022, 9:07 a.m.