RunEscape: Run escape ssGSEA

In bimberlabinternal/CellMembrane: A package with high-level wrappers and pipelines for single-cell RNA-seq tools

Run escape ssGSEA

Description

This will run escape to calcualte ssGSEA on Hallmark gene sets

Usage

RunEscape(
  seuratObj,
  outputAssayBaseName = "escape.",
  doPlot = FALSE,
  performDimRedux = FALSE,
  msigdbGeneSets = c("H", C5 = "GO:BP", C5 = "GO:MF"),
  customGeneSets = NULL,
  customGeneSetAssayName = "CustomGeneSet",
  maxBatchSize = 1e+05,
  nCores = 1
)

Arguments

seuratObj	A Seurat object.
outputAssayBaseName	The basename of the assay to store results. Escape will be run once for each gene set.
doPlot	If true, a FeaturePlot will be printed for each pathway
performDimRedux	If true, the standard seurat PCA/FindClusters/UMAP process will be run on the escape data. This may be most useful when using a customGeneSet or a smaller set of features/pathways
msigdbGeneSets	A vector containing gene set codes specifying which gene sets should be fetched from MSigDB and calculated. Some recommendations in increasing computation time: H (hallmark, 50 gene sets), C8 (scRNASeq cell type markers, 830 gene sets), C2 (curated pathways, 6366 gene sets), GO:BP (GO biological processes, 7658). Each item will be processed into a separate assay.
customGeneSets	A (preferably named) list containing gene sets to be scored by escape.
customGeneSetAssayName	The name for the output assay (prefixed with outputAssayBaseName) for any customGeneSets
maxBatchSize	If more than this many cells are in the object, it will be split into batches of this size and run in serial.
nCores	Passed to runEscape()

Value

The seurat object with results stored in an assay

bimberlabinternal/CellMembrane documentation built on June 9, 2025, 6:59 p.m.