Question: genlist for clusterprofiler
0
gravatar for archie
6 months ago by
archie60
India
archie60 wrote:

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

clusterprofiler • 442 views
ADD COMMENTlink modified 6 months ago by Guangchuang Yu1.9k • written 6 months ago by archie60
0
gravatar for Guangchuang Yu
6 months ago by
Guangchuang Yu1.9k
China/Hong Kong/The University of Hong Kong
Guangchuang Yu1.9k wrote:

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

ADD COMMENTlink written 6 months ago by Guangchuang Yu1.9k
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