sctype: Run the sctype approach as it's implemented by Ianevski, A.,...

In sccca: Single-Cell Correlation Based Cell Type Annotation

Run the sctype approach as it's implemented by Ianevski, A., Giri, A.K. and Aittokallio, T.

Description

This Function is used to run the sctype approach with faster implementation

Usage

sctype(sobj,assay="RNA",tissue,tt="a",clus,org="a",scaled=T,database="sctype")

Arguments

sobj	Seurat object.
assay	assay to be used default is set to RNA.
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.
clus	colname in the mata.data that have the cell cluster numbers.
org	organism to be used that can be 'h' for human, 'm' for mouse, and 'a' for all markers.
scaled	indicates whether the matrix is scaled (TRUE by default)
database	name of the database to be used that can be 'sctype' or 'UMD'

Value

vector of genes names which overlap with the correlation matrix.

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.