2 hours ago by
Hello. I am using clusterProfiler R package. I am trying to make a visualize result using a dotplot graph for my data.
It seems I am facing a stumbling block on the final analysis using compareCluster.
I am working with E. coliK12 strain and I want to perform an enrichment analysis with Kegg (enrichKEGG)
I wonder why my code is not working. The example of what I am trying to achieve is shown in this example link (yulab-smu.github.io/clusterProfiler-book/chapter11.html#formula-interface-of-comparecluster). Any ideas would be most appreciated. Thank you.
mydf <- data.frame(Entrez=names(geneQ), FC=geneQ)
head(mydf)
Entrez FC
1 946671 7.1331936
2 947072 5.7164422
3 944863 5.4384038
4 945322 3.8615915
5 948027 3.7971514
mydf <- mydf[abs(mydf$FC) > 1,]
mydf$group <- "upregulated"
mydf$group[mydf$FC < 0] <- "downregulated"
mydf$othergroup <- "A"
mydf$othergroup[abs(mydf$FC) > 2] <- "B"
formula_res <- compareCluster(Entrez~group+othergroup, data=mydf, fun="enrichKEGG")
No enrichment found in any of gene cluster, please check your input...
