jnhutchinson · July 27, 2017 18:54
diff --git a/custom_gsea.R b/custom_gsea.R
 # run clusterprofiler  
 all.results.gsea <- all.results[[1]]$stats.eset # these are all the statistical results from running DESeq2
 lfcs <- all.results.gsea$log2FoldChange # the log fold changes from the comparison
 names(lfcs) <- all.results.gsea$entrezID # I previously annotated the stats results with the entrezids using biomart
 lfcs <- sort(lfcs, decreasing=TRUE) 
 results = GSEA(lfcs, TERM2GENE=set2gene, minGSSize=200, maxGSSize=1700)  # my set2gene was just a two column dataframe with the geneset id in the first column and the entrez gene ids in the second
	# run clusterprofiler
	all.results.gsea <- all.results[[1]]$stats.eset # these are all the statistical results from running DESeq2
	lfcs <- all.results.gsea$log2FoldChange # the log fold changes from the comparison
	names(lfcs) <- all.results.gsea$entrezID # I previously annotated the stats results with the entrezids using biomart
	lfcs <- sort(lfcs, decreasing=TRUE)
	results = GSEA(lfcs, TERM2GENE=set2gene, minGSSize=200, maxGSSize=1700) # my set2gene was just a two column dataframe with the geneset id in the first column and the entrez gene ids in the second