KEGGHyperGParams-class {Category} | R Documentation |
Parameter classes for representing all parameters needed for
running the hyperGTest
method with KEGG or PFAM as the
category.
Objects can be created by calls of the form
new("KEGGHyperGParams", ...)
or
new("PFAMHyperGParams", ...)
.
geneIds
:"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
:"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
:cateogrySubsetIds
:"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
:pvalueCutoff
:testDirection
:"over"
) or
underrepresentation ("under"
).
Class "HyperGParams"
, directly.
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
.S. Falcon
HyperGResult-class
GOHyperGParams-class
geneKeggHyperGeoTest
hyperGTest