richGSEA-methods: richGSEA method

In guokai8/richR: Function Enrichment analysis and Network construction

richGSEA method

Description

richGSEA

Usage

richGSEA(
  x,
  object,
  keytype = "",
  pvalue = 0.05,
  padj = NULL,
  KEGG = FALSE,
  minSize = 15,
  ontology = "",
  maxSize = 500,
  padj.method = "BH",
  organism = NULL,
  table = TRUE,
  sep = ",",
  ...
)

Arguments

x	a vector include all log2FC with gene name
object	annotation file for all genes
pvalue	pvalue cutoff value
padj	adjust p value cut off method
KEGG	a logical evaluating to TRUE or FALSE indicating whether KEGG GSEA were peformed or not.
minSize	Minimal size of a gene set to test. All pathways below the threshold are excluded.
maxSize	Maximal size of a gene set to test. All pathways above the threshold are excluded.
padj.method	p value adjust method
table	leadingEdge as vector
sep	character string used to separate the genes when concatenating

Value

GSEAResult

Author(s)

Kai Guo

Examples

## Not run: 
set.seed(123)
hsako <- buildAnnot(species="human",keytype="SYMBOL",anntype = "KEGG")
name <- sample(unique(hsako$GeneID),1000)
gene<-rnorm(1000)
names(gene) <- name
res <- richGSEA(gene,object = hsako)

## End(Not run)

guokai8/richR documentation built on June 10, 2025, 4:51 a.m.