call_connectome: Function to call connectome with databases from OmniPath...

In saezlab/liana: LIANA: a LIgand-receptor ANalysis frAmework

Function to call connectome with databases from OmniPath [[DEPRECATED]]

Description

Function to call connectome with databases from OmniPath [[DEPRECATED]]

Usage

call_connectome(sce, op_resource = NULL, .format = TRUE, assay, ...)

Arguments

sce	Seurat object as input
op_resource	OmniPath Intercell Resource DN
.format	bool whether to format output
assay	assay name
...	dot params passed to connectome

Details

Stats: 1) The ‘weight_norm’ edge attribute is derived from the normalized expression of the ligand and the receptor in the single-cell data. 2) The ‘weight_scale’ edge attribute is derived from the z-scores of the ligand and the receptor in each edge, and is of higher value when the ligand and receptor are more specific to a given pair of cell types 3) DEG p-values for L and R

Value

An unfiltered connectome results df

saezlab/liana documentation built on Nov. 8, 2023, 11:53 a.m.