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,
  outputAssayName = "escape.ssGSEA",
  doPlot = FALSE,
  doPca = TRUE,
  performDimRedux = FALSE,
  msigdbGeneSets = c("H"),
  customGeneSets = NULL,
  assayName = "RNA"
)

Arguments

seuratObj	A Seurat object.
outputAssayName	The name of the assay to store results
doPlot	If true, a FeaturePlot will be printed for each pathway
doPca	boolean determining if the PCA plot should be computed and printed.
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).
customGeneSets	A (preferably named) list containing gene sets to be scored by escape.
assayName	The name of the source assay

Value

The seurat object with results stored in an assay

bimberlabinternal/CellMembrane documentation built on Oct. 16, 2024, 6:53 a.m.