call_italk: Run iTALK with OmniPath data [[DEPRECATED]]

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

Run iTALK with OmniPath data [[DEPRECATED]]

Description

Run iTALK with OmniPath data [[DEPRECATED]]

Usage

call_italk(sce, op_resource, assay = "RNA", .format = TRUE, ...)

Arguments

sce	Seurat object or SingleCellExperiment as input
op_resource	OmniPath Intercell Resource DN
assay	assay to use from Seurat object
.format	bool: whether to format output
...	Parameters passed to Seurat FindMarkers (ref requires import)

Details

In order to be comparable with the remainder of the methods, we calculate the mean of the ligand and receptor logFC. The original implementation only uses the DE genes above a certain logFC threshold.

Value

An unfiltered iTALK df sorted by relevance

In this case, we use the product of the logFC rather than thresholding, as in the original implementation.

saezlab/ligrec_decoupler documentation built on Aug. 10, 2024, 8:56 a.m.