enrichIt: Flexible GSEA for Precomputed Gene Lists

In ncborcherding/escape: Easy single cell analysis platform for enrichment

Flexible GSEA for Precomputed Gene Lists

Description

A convenience front-end to **fgsea** that lets you point at the 'avg_log2FC' and 'p_val_adj' columns coming out of Seurat / DESeq2 / edgeR etc. It converts them to a signed -log10(*p*) ranking, filters on significance / effect size, and then runs fgsea.

Usage

enrichIt(
  input.data,
  gene.sets,
  gene_col = NULL,
  logFC_col = "avg_log2FC",
  pval_col = c("p_val_adj", "p_val"),
  ranking_fun = c("signed_log10_p", "logFC"),
  pval_cutoff = 1,
  logFC_cutoff = 0,
  minSize = 5,
  maxSize = 500,
  padjust_method = "BH",
  nproc = 0
)

Arguments

input.data	Either • a named numeric vector **already ranked**, *or* • a data.frame/tibble with one row per gene and columns containing log-fold-change and *p*-value. If the gene ID is not in 'rownames(data)', supply 'gene_col'.
gene.sets	AA named list of character vectors, the result of [getGeneSets()], or the built-in data object [escape.gene.sets].
gene_col	Name of the column holding gene identifiers (ignored when they are row-names). Default 'NULL'.
logFC_col, pval_col	Column names for logFC and *p* (or adj.*p*) – defaults match Seurat’s 'FindMarkers()'.
ranking_fun	How to build the ranking: '"signed_log10_p"' (default) or '"logFC"'.
pval_cutoff, logFC_cutoff	Filters applied **before** ranking.
minSize, maxSize	Integer. Minimum / maximum pathway size passed to *fgsea* (default 5 / 500).
padjust_method	Multiple-testing correction; any method accepted by [stats::p.adjust()] (default '"BH"').
nproc	Passed to **fgsea** ('0' = multithread if OpenMP available).

Value

'data.frame' with the usual fgsea columns plus a convenient 'leadingEdge' character column collapsed with \";\".

See Also

[fgsea::fgsea()], [getGeneSets()], [gseaEnrichment()]

Examples

pbmc_small <- SeuratObject::pbmc_small

Seurat::Idents(pbmc_small) <- "groups"
markers <- Seurat::FindMarkers(pbmc_small, 
                               ident.1 = "g1", 
                               ident.2 = "g2")

gs <- list(Bcells = c("MS4A1", "CD79B", "CD79A", "IGH1", "IGH2"),
           Tcells = c("CD3E", "CD3D", "CD3G", "CD7","CD8A"))
               
gsea <- enrichIt(markers, 
                 gene.sets = gs)

ncborcherding/escape documentation built on June 12, 2025, 1 p.m.