ChrMapLinearMParams-class {Category} | R Documentation |
This class encapsulates parameters needed for testing systematic
variations in some gene-level statistic by chromosome bands using
linearMTest
.
Objects can be created by calls of the form
new("ChrMapLinearMParams", ...)
.
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"
,
indicating whether the test performed should be a conditional
test. geneStats
:"numeric"
,
giving the gene-level statistics to be used in the tests. universeGeneIds
:"ANY"
: A
vector of gene ids 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
:datPkg
:"DatPkg"
used to assist
with dispatch based on type of annotation data available. 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
:"GO"
.pvalueCutoff
:minSize
:testDirection
:"up"
) or decrease
("down"
) in the geneStats
values within a gene set
relative to the remaining genes.
Class "LinearMParams"
, directly.
signature(r = "ChrMapLinearMParams")
:
Accessor for the conditional
slot. signature(r = "ChrMapLinearMParams",
value = "logical")
: Replacement method for the
conditional
slot.
Deepayan Sarkar
showClass("ChrMapLinearMParams")