GOHyperGParams-class: Class "GOHyperGParams"
Description
A parameter class for representing all parameters needed for running
the hyperGTest method with one of the GO
ontologies (BP, CC, MF) as the category.
Objects from the Class
Objects can be created by calls of the form new("GOHyperGParams", ...).Slots
ontology:- A string specifying the GO ontology to use.
Must be one of "BP", "CC", or "MF".
conditional:- A logical indicating whether the
calculation should condition on the GO structure.
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".
datPkg:- Holds a DatPkg object which is of a
particular type that in turn varies with the kind of annotation
package this is.
pvalueCutoff:- A numeric values between zero and one
used as a p-value cutoff for p-values generated by the
Hypergeometric test. When the test being performed is
non-conditional, this is only used as a default value for
printing and summarizing the results. For a conditional
analysis, the cutoff is used during the computation to determine
perform the conditioning: child terms with a p-value less than
pvalueCutoff are conditioned out of the test for their parent
term.
testDirection:- A string which can be either "over"
or "under". This determines whether the test performed detects
over or under represented GO terms.
Extends
Class "HyperGParams", directly.Methods
hyperGTest(p)- 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. ontology(p), ontology(p) <- value- Accessors
for the GO ontology. When setting,
value should be one
of "BP", "CC", or "MF". conditional(p), conditional(p) <-
value- Accessors for the conditional flag. When setting,
value must be TRUE or FALSE.