enrichIt {escape} | R Documentation |
This function allows users to input both the single-cell RNA-sequencing counts and any gene set pathways either from the stored data or from other sources. The enrichment calculation itself uses the gsva R package and the poisson distribution for RNA.
enrichIt(obj, gene.sets = NULL, groups = 1000, cores = 2)
obj |
The count matrix, Seurat, or SingleCellExperiment object. |
gene.sets |
Gene sets from |
groups |
The number of cells to separate the enrichment calculation. |
cores |
The number of cores to use for parallelization. |
Data frame of normalized enrichmenet scores (NES)
Nick Borcherding, Jared Andrews
getGeneSets
to collect gene sets.
# download HALLMARK gene set collection GS <- getGeneSets(library = "H") GS <- GS[c(1:2)] #Reduce list size for example seurat_ex <- suppressWarnings(SeuratObject::pbmc_small) ES <- enrichIt(obj = seurat_ex, gene.sets = GS) # alternatively, construct your own list of gene sets myGS <- list(Housekeeping = c("ACTA1", "ACTN1", "GAPDH"), Cancer = c("TP53","BRCA2","ERBB2","MYC"))