[Bioc-devel] Fwd: Gostats and custom list

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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>
<+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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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099