process_clus: Gets the associated cell types using correlation-based...

In sccca: Single-Cell Correlation Based Cell Type Annotation

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]

sccca documentation built on May 29, 2024, 2:22 a.m.