compareGSEA: compare GSEA enrichment results across different samples and...

In hurlab/RichR: Function Enrichment analysis and Network construction

compare GSEA enrichment results across different samples and generate figure

Description

compare GSEA enrichment results across different samples and generate figure

Usage

compareGSEA(
  x,
  object,
  gene = NULL,
  pathway = NULL,
  mycol = NULL,
  pvalue = 0.05,
  padj = NULL,
  label = FALSE,
  gseaParam = 1,
  ticksSize = 0.2,
  ncol = 2,
  scales = "fixed"
)

Arguments

x	list of GSEAResult
object	Annot object
gene	list of a vector include all log2FC with gene name (optional)
pathway	pathways you want to display (optional)
mycol	a vector indicate the colors used for the figure
pvalue	cutoff value of pvalue (if padj set as NULL)
padj	cutoff value of p adjust value
label	display the NES values or not
scales	Should scales be fixed ("fixed", the default), free ("free"), or free in one dimension ("free_x", "free_y")?
top	number of terms you want to display,

Author(s)

Kai Guo

Examples

## Not run: 
hsako <- buildAnnot(species="human",keytype="SYMBOL",anntype = "KEGG")
gene1 <- sample(unique(hsako$GeneID),1000)
gene2 <- sample(unique(hsako$GeneID),1000)
fc1<-rnorm(1000,11,2)
names(fc1)<-gene1
fc2<-rnorm(1000,11,2)
names(fc2)<-gene2
resko1 <-richGSEA(fc1,kodata = hsako)
resko2 <-richGSEA(fc2,kodata = hsako)
res<-compareGSEA(list(S1=resko1,S2=resko2),hsako)

## End(Not run)

hurlab/RichR documentation built on Feb. 5, 2024, 8:07 p.m.