call_sca: Function to call SingleCellSignalR with databases from...

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

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

Description

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

Usage

call_sca(
  sce,
  op_resource,
  .format = TRUE,
  assay = "RNA",
  assay.type = "logcounts",
  ...
)

Arguments

sce	SingleCellExperiment or SeuratObject as input
op_resource	OmniPath Intercell Resource DN
.format	bool whether to format output
assay	Seurat assay data to use
assay.type	count slot (logcounts by default)
...	arguments passed to 'SCAomni::cell_signaling'

Details

Stats: LRScore = sqrt(LR product)/mean(raw counts) * sqrt(LR product) where expression of l > 0 and r > 0 LRScore = 1 is the highest (~ most likely hit), 0 is the lowest.

Value

An unfiltered SCA tibble

saezlab/liana documentation built on Aug. 10, 2024, 8:14 a.m.