CoHyperGParams-class {PCpheno} | R Documentation |
A parameter class for representing all parameters needed for running
the hyperGTest
method with multiprotein complexes.
Objects can be created by calls of the form new("CoHyperGParams",...)
.
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"
).signature(p =
"HyperGParams")
: Perform hypergeometric tests to
assess over-representation 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(r)
, geneIds(r) <- value
ontology(r)
pvalueCutoff(r)
, pvalueCutoff(r) <-
value
value
should be a numeric value between zero and one.testDirection
value
must be either "over" or "under".universeGeneIds(r)
isConditional(r)
TRUE
if the instance
has its conditional flag set
S. Falcon and N. LeMeur
HyperGResult-class
CoHyperGResult-class
hyperGTest