process_clus {sccca}

Gets the associated cell types using correlation-based approach

Description

This Function is used to get the associated cell clusters using correlation-based approach

Usage

process_clus(cluster,sobj,assay="RNA",clus,markers,cor_m,m_t=0.9,c_t=0.7,test="p")

Arguments

cluster

associated cluster name.

sobj

Seurat object.

assay

assay to be used default is set to RNA.

clus

cell clusters.

markers

cell markers database.

cor_m

gene correlation matrix.

m_t

overlap threshold between cell markers and expression matrix.

c_t

correlation threshold between genes.

test

statistical test that check if overlap is significant could be "p" for phyper or "f" for fisher.

Value

data frame of proposed cell types.

Author(s)

Mohmed Soudy [e-mail] and Sohpie LE BARS [e-mail] and Enrico Glaab [e-mail]