MSigDF.R

devtools::install_github("toledoem/msigdf")

setwd("TCGA-BRCA/")
library(msigdf)
library(dplyr)
library("ggnewscale")
library(clusterProfiler)
library(enrichplot)
library(ggplot2)
xxt<-read.table("selectmrna43id_fc")
head(xxt)
genelist<-as.numeric(t(xxt[,2]))
names(genelist) = as.character(t(xxt[,1]))
de <- names(genelist)
c <- msigdf.human %>% dplyr::select(geneset, symbol) %>% as.data.frame 
x <- enricher(de, TERM2GENE = c, pvalueCutoff=0.05)
cnetplot(x, showCategory = 5, foldChange=geneList)

a<-as.data.frame(genelist)
genelist<-as.numeric(a[1,])
names(genelist) = as.character(colnames(a))
genelist = sort(genelist, decreasing = TRUE)
y <- GSEA(genelist, TERM2GENE = c)


grep -Fwf selectmrna43 rowData_brca_data.txt > selectmrna43id
join <(sort selectmrna43id) <(sort selectmrna43_fc) | sed 's/\ /\t/g' | cut -f3,7> selectmrna43id_fc