Question: genlist for clusterprofiler
1
gravatar for archie
9 months ago by
archie70
India
archie70 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

ADD COMMENTlink modified 8 weeks ago by zx87546.1k • written 9 months ago by archie70
1
gravatar for Guangchuang Yu
9 months ago by
Guangchuang Yu2.0k
China/Hong Kong/The University of Hong Kong
Guangchuang Yu2.0k wrote:

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

ADD COMMENTlink written 9 months ago by Guangchuang Yu2.0k
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