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

Source: R/sca_pipe.R
call_sca.Rd

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`

Value

An unfiltered SCA tibble

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.