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Loading required package: graph
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: SparseM
Package SparseM (0.80) loaded.
To cite, see citation("SparseM")
Attaching package: 'SparseM'
The following object(s) are masked from package:stats :
model.response
The following object(s) are masked from package:base :
backsolve,
chol
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Building most specific GOs ..... ( 3 GO terms found. )
Build GO DAG topology .......... ( 7 GO terms and 6 relations. )
Annotating nodes ............... ( 4 genes annotated to the GO terms. )
-- Classic Algorithm --
the algorithm is scoring 6 nontrivial nodes
parameters:
test statistic: fisher
GO.ID Term Annotated Significant
1 GO:0042578 phosphoric ester hydrolase activity 2 2
2 GO:0016791 phosphatase activity 1 1
3 GO:0003674 molecular_function 4 2
4 GO:0003824 catalytic activity 4 2
5 GO:0016787 hydrolase activity 4 2
6 GO:0016788 hydrolase activity, acting on ester bond... 4 2
7 GO:0016298 lipase activity 2 0
Expected elimFisher
1 1.0 0.17
2 0.5 0.50
3 2.0 1.00
4 2.0 1.00
5 2.0 1.00
6 2.0 1.00
7 1.0 1.00
-> GO:0042578 (phosphoric ester hydrolase activity) : 0.1667
GeneA
GeneC
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