[Bioc-devel] Fwd: Gostats and custom list

[James W. MacDonald]

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On Tue, Apr 11, 2017 at 8:32 AM, amit kumar subudhi <amit4help at gmail.com>
wrote:

> Hi,
>
> I am using Gostats to perform GO enrichment from custom list of genes and
> custom annotations. My annotation file looks like this
> head (geneGO)
>       GOterm evi       GeneID
> 1 GO:0016020  ND PCHAS_010020
> 2 GO:0016021  ND PCHAS_010020
> 3 GO:0016020  ND PCHAS_010030
> 4 GO:0016021  ND PCHAS_010030
> 5 GO:0016020  ND PCHAS_010040
> 6 GO:0016021  ND PCHAS_010040
>
> My hyperGtest result looks like this
> >Over.bp.Phase_0_2 <-hyperGTest(params.bp.Phase_0_2 )
> >Over.bp.Phase_0_2
> Gene to GO BP Conditional test for over-representation
> 228 GO BP ids tested (45 have p < 0.05)
> Selected gene set size: 37
>     Gene universe size: 1707
>     Annotation package: Based on a GeneSetCollection Object
> and my summary result looks like this
>
> enrichgobp.Phase_9_12 <-summary(Over.bp.Phase_9_12 )
>        GOBPID       Pvalue OddsRatio    ExpCount Count
> Size                                              Term         V8
> 1  GO:0019362 4.441045e-05 17.239583  0.43350908     5   20
> pyridine nucleotide metabolic process Phase_0_2
> 2  GO:0046031 1.163932e-04 22.370370  0.28178090     4
> 13                             ADP metabolic process Phase_0_2
> 3  GO:0006096 1.163932e-04 22.370370  0.28178090     4
> 13                                glycolytic process Phase_0_2
> 4  GO:0016052 1.163932e-04 22.370370  0.28178090     4
> 13                    carbohydrate catabolic process Phase_0_2
> 5  GO:0009185 1.604285e-04 20.121212  0.30345636     4   14
> ribonucleoside diphosphate metabolic process Phase_0_2
> 6  GO:0009135 1.604285e-04 20.121212  0.30345636     4   14   purine
> nucleoside diphosphate metabolic process Phase_0_2
> 7  GO:0043436 2.085503e-04  5.450461  2.21089631     9
> 102                         oxoacid metabolic process Phase_0_2
> 8  GO:0006165 2.153810e-04 18.280992  0.32513181     4   15
> nucleoside diphosphate phosphorylation Phase_0_2
> 9  GO:0051186 1.523968e-03  7.114211  0.88680352     5
> 42                        cofactor metabolic process Phase_0_2
>
> what am I suppose to do, If I want to retrieve the geneIDs associated with
> each GOterms. The other information about params is
>
> params.bp.Phase_0_2<-GSEAGOHyperGParams(name="P.
> chabaudi",geneSetCollection=gsc,geneIds=Phase_0_2
> ,universeGeneIds=universe,ontology="BP",pvalueCutoff=0.
> 05,conditional=TRUE,
> testDirection="over")
>
> Looking forward to hear from you.
>
> With best regards, Amit
>
> --
> Amit Kumar Subudhi, PhD
> Post Doctoral Research Scientist,
> Pathogen Genomics Group,
> Division of Biological and Environmental Sciences and Engineering,
> Level 4, 4326-WS10, Building 2,
> King Abdullah University of Science and Technology (KAUST),
>
> Thuwal 23955-6900, Kingdom of Saudi Arabia,
> Phone: (+966 12) 808 0614 <+966%2012%20808%200614>, Mobile: (+966) 5
> 40375986,
> Email Address: amit.subudhi at kaust.edu.sa
>
>
>
> --
> Amit Kumar Subudhi, PhD
> Post Doctoral Research Scientist,
> Pathogen Genomics Group,
> Division of Biological and Environmental Sciences and Engineering,
> Level 4, 4326-WS10, Building 2,
> King Abdullah University of Science and Technology (KAUST),
>
> Thuwal 23955-6900, Kingdom of Saudi Arabia,
> Phone: (+966 12) 808 0614, Mobile: (+966) 5 40375986,
> Email Address: amit.subudhi at kaust.edu.sa
>
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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