genlist for clusterprofiler

Question

[Omics data mining]

Dear all,

I am using the clusterprofiler. I used the enrichGO, enrichKEGG and enrichDO .

data<-read.delim("enrich.txt")
genes<-data$entrez[abs(data$expr)>2]

I used genes as input in enrichGO,enirchKEGG. But I am not able to create input geneList for the gse function .

ego3 <- gseGO(geneList     = geneList,
              OrgDb        = org.Hs.eg.db,
              ont          = "CC",
              nPerm        = 1000,
              minGSSize    = 100,
              maxGSSize    = 500,
              pvalueCutoff = 0.05,
              verbose      = FALSE)

I have gene list with log2fold change. Therefore I also want to analyse ontology based on the gene set enrichment gseGO and gseKEGG functions.

Can anybody suggest me how to prepare this input file from tab seprated data file.

All suggestions will be appreciated.

Thank you

Answer 1

[Guangchuang Yu]

see the tutorial on https://github.com/GuangchuangYu/DOSE/wiki/how-to-prepare-your-own-geneList.

[Arindam Ghosh]

Is it necessary to use a ranked gene list for clusterProfiler. I have a gene list from different modules in a network for which I want to do annoation/ORA.