Hi all
I am trying to run HyperGTest on KEGG.

The help 'HyperGResult-accessors {Category}' describe count as:

"geneCounts
returns an "integer" vector: for each category term tested, the number of
genes from the gene set that are annotated at the term."


> hypTest <- new("KEGGHyperGParams", geneIds = dGenes,
+                annotation = "org.Mm.eg.db", pvalueCutoff = 0.05,
 testDirection='over')
> hypRes <- hyperGTest(hypTest)
> hypRes
Gene to KEGG  test for over-representation
147 KEGG ids tested (25 have p < 0.05)
Selected gene set size: 191
    Gene universe size: 5874
    Annotation package: org.Mm.eg
> goRes <- summary(hypRes)
> dim(goRes)
[1] 25  7
> head(goRes)
  KEGGID       Pvalue OddsRatio ExpCount Count Size
           Term
1  04020 2.602986e-08  4.987598 5.084193    21  178               Calcium
signaling pathway
2  04080 6.360363e-08  3.920560 7.911919    26  277 Neuroactive
ligand-receptor interaction
3...


My test shows that 21 of my genes are annotated with 'Calcium signaling
pathway'. However, when I check what are those genes I only get 7 and not
21. I am confused if I am doing it correctly.

I am using the following code to get all the genes (ENtrez IDs) for
'Calcium signaling pathway'


> k2name <- as.list(KEGGPATHID2NAME) #Mapping between kegg ID to kegg
pathway name
> k2name['04020']
$`04020`
[1] "Calcium signaling pathway"

>kpath <- as.list(org.Mm.egPATH2EG)
# Remove pathway identifiers that do not map to any entrez gene id
>kpath2Entrez <- kpath[!is.na(kpath)]

> kpath2Entrez['04020']
$`04020`
  [1] "11441"  "11513"  "11514"  "11515"  "11540"  "11541"  "11548"
 "11549"  "11550"  "11554"  "11555"  "11556"  "11607"  "11608"  "11739"
 [16] "11740"  "11937"  "11938"  "11941"  "12061"  "12062"  "12182"
 "12286"  "12287"  "12288"  "12289"  "12290"  "12291"  "12292"  "12313"
 [31] "12314"  "12315"  "12322"  "12323"  "12325"  "12326"  "12425"
 "12426"  "12494"  "12669"  "12671"  "13488"  "13492"  "13617"  "13618"
 [46] "13649"  "13866"  "13867"  "13869"  "14062"  "14672"  "14675"
 "14676"  "14680"  "14682"  "14683"  "14810"  "14811"  "14813"  "14814"
 [61] "14816"  "14829"  "15465"  "15466"  "15558"  "15559"  "15560"
 "15562"  "15563"  "15564"  "15565"  "15566"  "16438"  "16439"  "16440"
 [76] "16867"  "18125"  "18126"  "18127"  "18216"  "18430"  "18436"
 "18438"  "18439"  "18440"  "18573"  "18574"  "18575"  "18595"  "18596"
 [91] "18679"  "18682"  "18747"  "18749"  "18750"  "18751"  "18752"
 "18795"  "18796"  "18797"  "18798"  "18799"  "18802"  "18803"  "18821"
[106] "19055"  "19056"  "19057"  "19058"  "19059"  "19108"  "19204"
 "19216"  "19218"  "19220"  "19229"  "20190"  "20191"  "20192"  "20541"
[121] "20698"  "21336"  "21337"  "21338"  "21390"  "21924"  "21925"
 "22045"  "22063"  "22333"  "22334"  "22335"  "26361"  "53313"  "54140"
[136] "54652"  "56398"  "56632"  "57260"  "58226"  "58861"  "67738"
 "67972"  "68961"  "70086"  "70261"  "70405"  "72469"  "73333"  "74055"
[151] "80796"  "94045"  "102093" "104110" "104111" "107589" "108058"
"108071" "110094" "110891" "110893" "114875" "170732" "210044" "213435"
[166] "213788" "228139" "228550" "228785" "231602" "234779" "239556"
"243764" "320404" "320707" "381290" "432530" "494124"




 intersect(kpath2Entrez['04020'], ourGenes) #results in only 7 genes.

Thanks

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