| Identify_CellType {CACIMAR} | R Documentation |
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)