虽然我不喜欢DAVID，但很多用户喜欢，所以clusterProfiler也支持了，最近github上又有人要求支持自定义背景。

Dear Guangchuang,

I am using clusterProfiler in Kegg pathway enrichment analysis, it is useful and nice. I am looking for a function which accept background and has ability to deal with Ensembl gene ID.

In a function enrichDAVID it can takes ensembl gene id as an input format, but not allows to enter background. enrichDAVID(gene = gene, idType="ENSEMBL_GENE_ID", annotation="KEGG_PATHWAY", species= "hsa")

Other command enrichKEGG has a background input but only takes entrez gene id, enrichKEGG(gene, organism = "hsa", keyType = "kegg", universe)

I have tried to convert my ensembl gene IDs to entrez gene id, but some ensembl gene IDs represent more than one entrez gene ID. I downloaded KEGG pathway dataset to apply fisher exact test. however, genes are in entrez ID and i am still dont know how to convert.

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clusterProfiler was used to visualize DAVID results in a paper published in BMC Genomics.

Some users told me that they may want to use DAVID at some circumstances. I think it maybe a good idea to make clusterProfiler supports DAVID, so that DAVID users can use visualization functions provided by clusterProfiler.

require(DOSE)
require(clusterProfiler)
data(geneList)
gene = names(geneList)[abs(geneList) > 2]
david = enrichDAVID(gene = gene, idType="ENTREZ_GENE_ID", 
listType="Gene", annotation="KEGG_PATHWAY")



> summary(david)
               ID            Description GeneRatio  BgRatio       pvalue
hsa04110 hsa04110             Cell cycle     11/68 125/5085 4.254437e-06
hsa04114 hsa04114         Oocyte meiosis     10/68 110/5085 1.119764e-05
hsa03320 hsa03320 PPAR signaling pathway      7/68  69/5085 2.606715e-04
             p.adjust qvalue                                             geneID
hsa04110 0.0003998379     NA 9133/4174/890/991/1111/891/7272/8318/4085/983/9232
hsa04114 0.0005261534     NA    9133/5241/51806/3708/991/891/4085/983/9232/6790
hsa03320 0.0081354974     NA                 4312/2167/5346/5105/3158/9370/9415
         Count
hsa04110    11
hsa04114    10
hsa03320     7

There are only 5085 human genes annotated by KEGG, this is due to out-of-date DAVID data.

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