[Bioc-devel] Fwd: Gostats and custom list

[amit kumar subudhi]

Sorry and thanks for the information.

On 11 Apr 2017 6:00 p.m., "James W. MacDonald" <jmacdon at uw.edu> wrote:

> This list is intended for discussions about package development, not
> general queries. Please post that sort of question on the support site,
> https://support.bioconductor.org
>
> 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>
>> <+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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