compare_GSE.HTSAnalyzer: Perform GSEA across multiple groups (1 vs other)

In ProfessionalFarmer/loonR: Common function in bioinformatics analysis

Perform GSEA across multiple groups (1 vs other)

Description

Perform GSEA across multiple groups (1 vs other)

Usage

compare_GSE.HTSAnalyzer(
  rna.df.log,
  group,
  prefix = "Group",
  customGS = NULL,
  exp.gene.type = "ENSEMBL",
  cutoff.log10 = 3,
  cal.auc = FALSE,
  permutation = 1000
)

Arguments

prefix	Default "Group"
customGS	User customed gene set. qusage::read.gmt. Should be converted to ENTREZID
exp.gene.type	RNA expression ID ENSEMBL. keytypes(org.Hs.eg.db)
cutoff.log10	Default 3. Minimux or maximum log10 value. Useful when meet inf or draw heatmap
cal.auc	If calcuate AUC value
permutation	Number of permutation

Examples

This function will perform GSEA analysis. Default geneset: GOBP, C2, C5, KEGG, HALLMARK

ProfessionalFarmer/loonR documentation built on Oct. 9, 2024, 9:56 p.m.