sccca: Run the pipeline for the cell type assignment

In sccca: Single-Cell Correlation Based Cell Type Annotation

Run the pipeline for the cell type assignment

Description

This Function is used to run the main pipeline that does the cell type assignment

Usage

sccca(sobj,assay="RNA",cluster,marker,tissue,tt="a",cond,m_t=0.9,c_t=0.7,test="p",org="a")

Arguments

sobj	Seurat object.
assay	assay to be used default is set to RNA.
cluster	colname in the mata.data that have the cell cluster numbers.
marker	cell markers database path.
tissue	specified tissue from which the data comes.
tt	tissue type whether 'a' for all types 'n' for normal tissues only or "c" for cancer tissues.
cond	colname in the meta.data that have the condition names.
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.
org	organism to be used that can be 'h' for human, 'm' for mouse, and 'a' for all markers.

Value

list of Seurat object that have the assigned clusters, and top 3 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.