05-富集分析(2)_GSEA

一步运行

## complete GSEA module
data_gse <- runGSEA(data_hyper,dir = "gse_out",
                       GO = TRUE,
                       KEGG = TRUE)

分步运行

计算

## step only resolve
data_gse <- gseResolve(
  data_hyper, 
  GO = FALSE, 
  KEGG = TRUE)

结果整理

## step summary results
gseSummary(
  data_gse, 
  dir = "gse_out", 
  prefix = "4-runGSEA", 
  top = 10)

辅助工具

自定义GO注释的富集分析

gseGO2(
  geneList,
  ont = "ALL",
  TERM2GENE,
  TERM2NAME = NA,
  organism = "UNKNOW",
  keyType = "SYMBOL",
  exponent = 1,
  minGSSize = 10,
  maxGSSize = 500,
  eps = 1e-10,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  verbose = TRUE,
  seed = FALSE,
  by = "fgsea",
  ...
)

可视化工具

gsea 图

p_gsea_list <- GSEAplot(gsob,top = 10)
down_plots_pdf <- "GO_limma_gseplot_down.pdf"
pdf(down_plots_pdf,height = 3,width = 4)
invisible(lapply(p_gsea_list[["down_plots"]], print))
dev.off()

gse 柱状图

gsob <- gseRes(data_gse)[["gseGO_res"]][["limma"]]
p_gsegbar <- GSEAbar(gsob,top = 10)
ggplot2::ggsave(p_gsegbar,filename = "gse_GO_bar.pdf", width = 3000,height = 3600,units = "px",limitsize = FALSE,device = cairo_pdf)