gravatar for LacquerHed

2 hours ago by

Wondering how I can get a list of the genes I submitted that fall within each category/term represented on the eventual dotplot. Thanks.

library(clusterProfiler)
library(enrichplot)
library(ggplot2)
organism = org.Mm.eg.db
library(org.Mm.eg.db)


df = read.csv("subcluster3_001_genes.csv", header=TRUE)


original_gene_list <- df$log2FoldChange


names(original_gene_list) <- df$GENENAME


gene_list<-na.omit(original_gene_list)


gene_list = sort(gene_list, decreasing = TRUE)

gse <- gseGO(geneList=gene_list, 
             ont ="ALL", 
             keyType = "SYMBOL", 
             minGSSize = 3, 
             maxGSSize = 800, 
             pvalueCutoff = .05, 
             verbose = TRUE, 
             OrgDb = organism, 
             pAdjustMethod = "none")


gse_simplified <- simplify(gse, cutoff=0.5, by="pvalue", select_fun=min)

require(DOSE)

dotplot(gse_simplified, showCategory=10, split=".sign") + facet_grid(.~.sign)

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modified 1 hour ago

written
2 hours ago
by

LacquerHed0



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