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)
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.
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.