run_enrichment

run_enrichment

run_enrichment(x, ...)

# S3 method for data.frame
run_enrichment(
  x,
  type = "kegg",
  group.by = "cluster",
  use.column = "entrezgene",
  org = "Mm",
  FDR = 0.01,
  p.adjust.method = "bonferroni",
  ...
)

Arguments

x

an object with DEGs.

...

arguments passed down to methods.

type

which ontology to use for enrichment (default: KEGG).

group.by

which variable to use for grouping (default: cluster).

use.column

which column contains entrez gene identifiers (default: entrezgene).

org

organisms (default: Mm).

FDR

cutoff for selection of DEG used for enrichment.

p.adjust.method

method to adjust p.values from enrichment (default: bonferroni).