run_enrichment: run_enrichment

In ddiez/scmisc: Miscellaneus Tools for the Analysis of Single Cell Data

run_enrichment

Description

run_enrichment

Usage

run_enrichment(x, ...)

## S3 method for class 'data.frame'
run_enrichment(
  x,
  type = "kegg",
  group.by = "cluster",
  use.column = "entrezgene",
  org = "Mm",
  lfc = 1,
  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).
lfc	avg_log2FC cutoff for selection of DEG used for enrichment.
fdr	p_val_adj cutoff for selection of DEG used for enrichment.
p.adjust.method	method to adjust p.values from enrichment (default: bonferroni).

ddiez/scmisc documentation built on July 21, 2024, 11:35 a.m.