HyperGResult-class: Class "HyperGResult"
Description
This class represents the results of a test for over-representation of
categories among genes in a selected gene set based upon the
Hypergeometric distribution. The hyperGTest
generic function returns an instance of the
HyperGResult class. For details on accessing
the results, see HyperGResult-accessors.
Objects from the Class
Objects can be created by calls of the form new("HyperGResult", ...).Slots
pvalues:"numeric" vector: the ordered
p-values for each category term tested.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. annotation:- A string giving the name of the chip
annotation data package used.
geneIds:- Object of class
"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:- A string identifying the testing method
used.
pvalueCutoff:- Numeric value used a a p-value
cutoff. Used by the
show method to count number of
significant terms.
testDirection:- A string indicating whether the
test should be for overrepresentation (
"over") or
underrepresentation ("under"). oddsRatios- a
"numeric" vector giving
the odds ratio for each category term tested. - expectedCounts
- a
"numeric" vector
giving the expected number of genes in the selected gene list to
be found at each tested category term.
Extends
Class "HyperGResultBase", directly.