parGSEA: GSEA Enrichment analysis function for data frame with log2FC...

In guokai8/richR: Function Enrichment analysis and Network construction

GSEA Enrichment analysis function for data frame with log2FC and name specifc

Description

GSEA Enrichment analysis function for data frame with log2FC and name specifc

Usage

parGSEA(
  x,
  object,
  log2FC = "log2FoldChange",
  gene.col = NULL,
  simplify = FALSE,
  keytype = "",
  pvalue = 0.05,
  padj = NULL,
  KEGG = FALSE,
  minSize = 15,
  ontology = "",
  maxSize = 500,
  padj.method = "BH",
  organism = NULL,
  table = TRUE,
  sep = ","
)

Arguments

x	data.frame include the gene name and log2FC
object	annotation file for all genes
log2FC	the column name for log2FoldChange
gene.col	the gene name column if rownames won't be used as gene name
simplify	boolean value to indicate if the simple table shoule be returned
pvalue	pvalue cutoff value
padj	adjust p value cut off method
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

Author(s)

Kai Guo

Examples

## Not run: 
hsako<-buildAnnot(species="human",keytype="SYMBOL",anntype = "KEGG")
hsako<-as.data.frame(hsako)
name=sample(unique(hsako$GeneID),1000)
gene<-rnorm(1000)
names(gene)<-name
d<-data.frame(Gene=name,log2FoldChange=gene)
rownames(d)<-d$Gene
res<-parGSEA(d,object = hsako)

## End(Not run)

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