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)
