ChrMapHyperGResult-class {Category} | R Documentation |
This class represents the results of a Hypergeometric test for
over-representation of genes in a selected gene list in the
chromosome band annotation. The hyperGTest
function returns
an instance of ChrMapHyperGResult
when given a parameter
object of class ChrMapHyperGParams
. For details on accessing
the results, see HyperGResult-accessors.
Objects can be created by calls of the form new("ChrMapHyperGResult", ...)
.
pvalue.order
:"integer"
that
gives the order of the p-values.conditional
:"logical"
is a flag indicating whether or not this result is from a
conditional analysis. chrGraph
:"graph"
. The nodes
are the chromosome bands with edges representing the tree
structure of the bands. Each node has a "geneIds"
attribute that gives the gene IDs annotated at that band.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.
testDirection
:"character"
indicating whether the test was for over-representation
("over"
) or under-representation ("under"
).
Class "HyperGResultBase"
, directly.
Seth Falcon
showClass("ChrMapHyperGResult") ## For details on accessing the results: ## help("HyperGResult-accessors")