KEGGHyperGParams-class: Class "KEGGHyperGParams" and "PFAMHyperGParams"
Description
Parameter classes for representing all parameters needed for
running the hyperGTest method with KEGG or PFAM as the
category.
Objects from the Class
Objects can be created by calls of the form
new("KEGGHyperGParams", ...) or
new("PFAMHyperGParams", ...).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.
cateogrySubsetIds:- 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.
This will be automatically set to "KEGG" or "PFAM" via the
class's prototype.
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").
Extends
Class "HyperGParams", directly.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.