HyperGParams-class: Class "HyperGParams"
Description
An abstract (VIRTUAL) parameter class for representing all parameters
needed by a method specializing the hyperGTest
generic. You should only use subclasses of this class directly.
Objects from the Class
Objects of this class cannot be instantiated directly.Slots
geneIds:- Object of class
"ANY": A vector of
gene identifiers. Numeric and character vectors are probably the
only things that make sense. These are the gene ids for the
selected gene set. universeGeneIds:- Object of class
"ANY": A
vector of gene ids in the same format as geneIds defining a
subset of the gene ids on the chip that will be used as the
universe for the hypergeometric calculation. If this is
NULL or has length zero, then all gene ids on the chip will
be used. annotation:- A string giving the name of the
annotation data package for the chip used to generate the data.
categorySubsetIds:- Object of class
"ANY":
If the test method supports it, can be used to specify a subset of
category ids to include in the test instead of all possible
category ids. categoryName:- A string describing the category.
Usually set automatically by subclasses. For example "GO".
pvalueCutoff:- The p-value to use as a cutoff for
significance for testing methods that require it. This value
will also be passed on to the result instance and used for
display and counting of significant results. The default is
0.01.
testDirection:- A string indicating whether the test
should be for overrepresentation (
"over") or
underrepresentation ("under"). datPkg:- Holds a DatPkg object which is of a
particular type that in turn varies with the kind of annotation
package this is.
Methods
- hyperGTest
signature(p =
"HyperGParams"): Perform hypergeometric tests to
assess overrepresentation of category ids in the gene set. See the
documentation for the generic function for details. This method
must be called with a proper subclass of
HyperGParams.geneIds(object), geneIds(object) <- value- Accessors for
the gene identifiers that will be used as the selected gene
list.
- codeannotation(object)
- Accessor for annotation. If you want
to change the annotation for an existing instance, use the
replacement form.
ontology(object)- Accessor for GO ontology.
organism(object)- Accessor for the organism character
string used as an identifier in
DatPkg. pvalueCutoff(r), pvalueCutoff(r) <-
value- Accessor for the p-value cutoff. When setting,
value should be a numeric value between zero and one. testDirection- Accessor for the test direction. When setting,
value must be either "over" or "under". universeGeneIds(r)- accessor for vector of gene
identifiers.