do_gsea: Do gsea

In wt12318/Easy_Bioinfo: Make some common bioinformatic workfolw easier to operate

Do gsea

Description

Do gsea

Usage

do_gsea(dt, gene_set, gene_id, stat)

Arguments

dt	dataframe contain gene id (gene_id) and rank statistics (stat)
gene_set	pathway information, the path of gmt file
gene_id	colname of gene_id
stat	colname of stat

Value

ES

Examples

res <- deg_deseq2(count_df,control_label="ctrl",control_counts=2,treatment_lable="KD",treatment_counts=2,parallel = TRUE,ncores = 4)
res$gene <- rownames(res)
gmt.file <- system.file("extdata", "h.all.v7.4.symbols.gmt", package="EasyBioinfo")
gsea_res <- do_gsea(res,gene_set = gmt.file,gene_id = "gene",stat = "stat")

wt12318/Easy_Bioinfo documentation built on June 17, 2022, 9:22 a.m.