FGSEA_GSEA_loop: Create GSEA loop

In HCGB-IGTP/HCGB.IGTP.DAnalysis: Useful in-house functions for multiple analysis

Create GSEA loop

Description

Plots GSEA results using ggplot and enrichment score provided

Usage

FGSEA_GSEA_loop(
  table_annot,
  folder_out,
  name_given,
  nproc_given,
  dataSet.list,
  GENE_SYMBOL.col = "GENE_SYMBOL",
  ranker.list = c("log2FoldChange", "signed.logPval"),
  padj.thres = 0.25,
  create.signed.logPval = FALSE
)

Arguments

table_annot	table to get results
folder_out	folder to store results
name_given	name for the comparison
nproc_given	threads to use
dataSet.list	list of GSEA datasets
GENE_SYMBOL.col	name of the hgnc column
ranker.list	columns to use for ranking
padj.thres	Pvalue adjusted threshold

HCGB-IGTP/HCGB.IGTP.DAnalysis documentation built on April 13, 2025, 12:03 a.m.