ChrMapHyperGParams-class {Category} | R Documentation |
This class encapsulates parameters needed for Hypergeometric testing
of over or under representation of chromosome bands among a selected
gene list using hyperGTest
.
Objects can be created by calls of the form new("ChrMapHyperGParams", ...)
.
chrGraph
:"graph"
. The nodes
are the chromosome bands and the edges describe the tree structure
of the bands. Each node has a "geneIds" node attributes (see
nodeData
) which contains a vector of gene IDs annotated at
the given band.conditional
:"logical"
~~ 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"
).datPkg
:"DatPkg"
used to
assist with dispatch based on type of annotation data available.
Class "HyperGParams"
, directly.
No methods defined with class "ChrMapHyperGParams" in the signature.
Seth Falcon
showClass("ChrMapHyperGParams")