Question: clusterProfiler GeneRatio minGSSize
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gravatar for zhang.jianhai
9 months ago by
zhang.jianhai0 wrote:

Hello,

I am using "enrichKEGG" on rice genes. The entriz ids are entr <- c("4337100", "4336350", "4324731", "4336393", "4347034", "4345789", "4336561", "107276072", "4324047", "4352785", "4344600", "4327916", "4328844", "4336915", "4338072", "4339251", "4325336", "4329887", "107276640", "9266093", "9270198", "4346096", "4343818"). kk <- enrichKEGG(gene=entr, organism="osa", minGSSize=5, pvalueCutoff=0.05, pAdjustMethod = "BH").

The result is data.frame(kk):

               ID                        Description GeneRatio BgRatio
osa00430 osa00430 Taurine and hypotaurine metabolism       1/4 21/4948
osa00941 osa00941             Flavonoid biosynthesis       1/4 25/4948
osa03020 osa03020                     RNA polymerase       1/4 46/4948

             pvalue   p.adjust     qvalue  geneID Count
osa00430 0.01687387 0.04012714 0.01055977 4344600     1
osa00941 0.02006357 0.04012714 0.01055977 4337100     1
osa03020 0.03668235 0.04890979 0.01287100 4325336     1

My questions are: 1. The minGSSize=5, but why only 1 gene is enriched, as shown in the "GeneRatio" "1/4"? 2. The pAdjustMethod is "BH", then it produces "qvalue", so how does "p.adjust" come out?

Regards

enrichkegg generatio • 172 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by zhang.jianhai0
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