Skip to content

Instantly share code, notes, and snippets.

@GuangchuangYu

GuangchuangYu/msigdf_clusterprofiler.R

Created August 17, 2016 17:14
Show Gist options
  • Save GuangchuangYu/11aa78d75711b76afd7467fb96a0a578 to your computer and use it in GitHub Desktop.
Save GuangchuangYu/11aa78d75711b76afd7467fb96a0a578 to your computer and use it in GitHub Desktop.
Download ZIP
Raw
msigdf_clusterprofiler.R
## devtools::install_github("stephenturner/msigdf")
library(msigdf)
library(dplyr)
library(clusterProfiler)
c2 <- msigdf.human %>%
filter(collection == "c2") %>% select(geneset, entrez) %>% as.data.frame
data(geneList)
de <- names(geneList)[1:100]
x <- enricher(de, TERM2GENE = c2)
y <- GSEA(geneList, TERM2GENE = c2)
head(x)
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment