CoHyperGResult-class {PCpheno} | R Documentation |
This class represents the results of a test for over-representation of genes in a selected gene set based among protein complexes upon the Hypergeometric distribution.
Objects is created by calls to the funtion hyperGTest.
pvalues
:"numeric"
vector: the ordered
p-values for each category term tested.
oddsRatios
:Object of class "numeric"
Odds ratio for each category term tested
expectedCounts
:Object of class "numeric"
The expected number of genes for each gene term tested
geneCounts
:"integer"
vector: for each
category term tested, the number of genes from the gene set that
are annotated at the term.
universeCounts
:"integer"
vector: for
each category term tested, the number of genes from the gene
universe that are annotated at the term.
catToGeneId
:Object of class "list"
. The
names of the list are category IDs. Each element is a vector
of gene IDs annotated at the given category ID and in the
specified gene universe.
Class "HyperGResultBase"
, directly.
signature(r =
"CoHyperGResult")
: return an "numeric"
vector: for each category term tested, the number of genes from
the gene set that are annotated at the term.
signature(r =
"HyperGResult")
: return a "numeric"
vector: the ordered p-values for each category term tested.
signature(r =
"HyperGResult")
: return a "numeric"
vector: the odds ratio for each category term tested.
signature(r =
"HyperGResult")
: return a "numeric"
vector: the expected number of genes for each GO term tested.
signature(r =
"HyperGResult")
: return an "numeric"
vector: for each category term tested, the number of genes from
the gene universe that are annotated at the term.
signature(r =
"CoHyperGResult")
: return a list named by the
protein Complexes. Each element of the list is a vector of gene
identifiers (from the gene universe) annotated at the
corresponding protein complex.
signature(r = "CoHyperGResult")
:
Returns a data.frame
summarizing the test result.
Optional arguments pvalue
and categorySize
allow
specification of minimum p-value and cateogyrSize, respectively.
Optional argument htmlLinks
is a logical value indicating
whether to add HTML links (useful in conjunction with xtables
print method with type
set to "html"
).
S. Falcon and N. LeMeur
data(DudleyPhenoM) data(ScISIC) ## Select genes sensitive to paraquat DudleyPhenoL <- apply(DudleyPhenoM,2,function(x) names(which(x==1))) paraquat <- DudleyPhenoL[["Paraq"]] ## Apply a hypergeometric test params <- new("CoHyperGParams", geneIds=paraquat, universeGeneIds=rownames(ScISIC), annotation="org.Sc.sgd.db", categoryName="ScISIC", pvalueCutoff=0.01, testDirection="over") paraquat.complex <- hyperGTest(params) ## access the p-values pvalues(paraquat.complex)[1:5] ## Display a summary of the results summary(paraquat.complex)[,1:4]