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Mary Kindall
▴
70
@mary-kindall-5600
Last seen 10.2 years ago
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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