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.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
:"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.annotation
:geneIds
:"ANY"
: the input
vector of gene identifiers intersected with the universe of gene
identifiers used in the computation. The class of this slot is
specified as "ANY"
because gene IDs may be integer or
character vectors depending on the annotation package.testName
:pvalueCutoff
:show
method to count number of
significant terms.
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]