This Function is used to run the main pipeline that does the cell type assignment
sccca(sobj,assay="RNA",cluster,marker,tissue,tt="a",cond,m_t=0.9,c_t=0.7,test="p",org="a")list of Seurat object that have the assigned clusters, and top 3 proposed cell types.
Seurat object.
assay to be used default is set to RNA.
colname in the mata.data that have the cell cluster numbers.
cell markers database path.
specified tissue from which the data comes.
tissue type whether 'a' for all types 'n' for normal tissues only or "c" for cancer tissues.
colname in the meta.data that have the condition names.
overlap threshold between cell markers and expression matrix.
correlation threshold between genes.
statistical test that check if overlap is significant could be "p" for phyper or "f" for fisher.
organism to be used that can be 'h' for human, 'm' for mouse, and 'a' for all markers.
Mohmed Soudy Mohamed.soudy@uni.lu and Sohpie LE BARS sophie.lebars@uni.lu and Enrico Glaab enrico.glaab@uni.lu