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Run Over-Representation Analysis and Plot Results

RunEnrichment.Rd

Runs over-representation analysis (ORA) using enrichR on a gene list or on significant DEGs from a data frame, then automatically calls PlotEnrichment to visualize the results. When group_column is supplied, analysis is run separately per group.

Usage

RunEnrichment(
  features = NULL,
  deg_df = NULL,
  gene_column = NULL,
  fc_column = NULL,
  padj_column = NULL,
  group_column = NULL,
  fc_cutoff = 0.25,
  padj_cutoff = 0.05,
  direction = "up",
  databases = c("MSigDB_Hallmark_2020", "GO_Biological_Process_2023", "KEGG_2021_Human"),
  top_n_plot = 20,
  plot_type = "dot",
  padj_cutoff_plot = 0.05,
  output_dir = NULL,
  object_name = "",
  subset_name = ""
)

Arguments

features

Character vector of gene symbols to test. Provide either this or deg_df, not both.

deg_df

Data frame of DE results (presto or FindMarkers). Genes are filtered by fc_cutoff, padj_cutoff, and direction before testing.

gene_column

Gene name column in deg_df. Auto-detected if NULL.

fc_column

logFC column in deg_df. Auto-detected if NULL.

padj_column

Adjusted p-value column. Auto-detected if NULL.

group_column

Column in deg_df to loop over (e.g. "group"). NULL = test all significant genes together.

fc_cutoff

Minimum absolute logFC to include a gene. Default 0.25.

padj_cutoff

Maximum adjusted p-value cutoff. Default 0.05.

direction

Which DEGs to test: "up" (logFC > 0), "down" (logFC < 0), or "both". Default "up".

databases

Character vector of enrichR database names to query. See enrichR::listEnrichrDbs() for all options. Default: c("MSigDB_Hallmark_2020", "GO_Biological_Process_2023", "KEGG_2021_Human").

top_n_plot

Maximum number of terms to show per database. Default 20.

plot_type

Type of plot passed to PlotEnrichment. Default "dot".

padj_cutoff_plot

Significance cutoff for filtering enrichment results before plotting. Default 0.05.

output_dir

Directory to save PDFs and result CSVs. NULL = no save, print only.

object_name

Label prefix for output file names.

subset_name

Optional subset label.

Value

A nested list: [[group]][[database]] containing enrichR result data frames. Invisibly when output_dir is set.

See also

PlotEnrichment, PlotVolcano