| sccca {sccca} | R Documentation |
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 Mohamed.soudy@uni.lu and Sohpie LE BARS sophie.lebars@uni.lu and Enrico Glaab enrico.glaab@uni.lu