scape {scaper} | R Documentation |
Cytokine activity scores for a normalized matrix.
Description
Computes cell-level estimates of cytokine activity for a normalized scRNA-seq
count matrix using the SCAPE method. SCAPE activity estimates are computed by scoring weighted genes
sets from the CytoSig or Reactome databases using the VAM::vamForCollection()
function. Individual gene sets for subsequent scoring can be reconstructed using
the genesetCytoSig
and the genesetReactome
functions
for the CytoSig and the Reactome database, respectively.
Usage
scape(counts.matrix, database = "cytosig", cytokine = "all")
Arguments
counts.matrix |
A |
database |
Database used for gene set construction and set scoring.
|
cytokine |
Vector of cytokine names to score for activity. The default value
of "all" will score all 41 cytokines supported by CytoSig or 31 supported by Reactome. Please see
function |
Value
A m x p
matrix consisting of the cell-level cytokine activity scores for p
cytokines.
See Also
genesetCytoSig
, genesetReactome
Examples
library(Seurat)
library(SeuratObject)
pbmc_small <- NormalizeData(pbmc_small)
counts.matrix <- as.data.frame(t(as.matrix(pbmc_small@assays$RNA@data)))
CytoSig.score.output <- scape(counts.matrix = counts.matrix,
database = "cytosig")
head(CytoSig.score.output)[,1:3]
CytoSig.score.output.specific <- scape(counts.matrix = counts.matrix,
database = "cytosig", cytokine = c("IL4", "IL13"))
head(CytoSig.score.output.specific)