HyperGTest 'count' value
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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 [[alternative HTML version deleted]]
Annotation Category Annotation Category • 1.0k views
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Mary Kindall ▴ 70
@mary-kindall-5600
Last seen 10.2 years ago
Working... Mistake in code Thanks On Mon, Nov 12, 2012 at 10:37 AM, Mary Kindall <mary.kindall@gmail.com>wrote: > 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 > > -- ------------- Mary Kindall Yorktown Heights, NY USA [[alternative HTML version deleted]]
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