R: Helper function for constructing a GOHyperGParams objects or...
GSEAGOHyperGParams
R Documentation
Helper function for constructing a GOHyperGParams objects or
KEGGHyperGParams objects from a GeneSetCollection
Description
Helps to create A parameter class for representing all parameters
needed for running the hyperGTest method. If it is a
GOHyperGParams object, being made, then with one of the GO ontologies
(BP, CC, MF) as the category. This function will construct the
parameter object from a GeneSetCollection object and if necessary will
also try to check to make sure that the object is based on a GO2ALL
mapping.
A GeneSetCollection Object. If a
GOHyperGParams object is sought, then this GeneSetCollection
should be based on a GO2ALLFrame object and so the idType of that
GeneSetCollection should be GOAllFrameIdentifier. If a
KEGGHyperGParams object is sought then a GeneSetCollection based
on a KEGGFrame object should be used and the idType will be a
KEGGFrameIdentifier.
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.
ontology
A string specifying the GO ontology to use.
Must be one of "BP", "CC", or "MF". (used with GO only)
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.
conditional
A logical indicating whether the
calculation should condition on the GO structure. (GO only)
testDirection
A string which can be either "over"
or "under". This determines whether the test performed detects
over or under represented GO terms.
...
optional arguments to configure the GOHyperGParams object.