LinearMParams-class: Class "LinearMParams"
Description
A parameter class for representing all parameters
needed by a method specializing the linearMTest generic.
Objects from the Class
Objects can be created by calls of the form
new("LinearMParams", ...).Slots
geneStats:- Named vector of class
"numeric",
giving the gene-level statistics to be used in the tests. The
names should correspond to the gene identifiers in gsc. universeGeneIds:- Object of class
"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. Currently this parameter is
ignored by the base linearMTest method. annotation:- A string giving the name of the
annotation data package for the chip used to generate the data.
datPkg:- Object of class
"DatPkg" used to assist
with dispatch based on type of annotation data
available. Currently this parameter is ignored by the
base linearMTest method. categorySubsetIds:- Object of class
"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. Currently this parameter is ignored by the
base linearMTest method. categoryName:- A string describing the category.
Usually set automatically by subclasses. For example
"ChrMap". pvalueCutoff:- The p-value to use as a cutoff for
significance for testing methods that require it. This value will
also be passed on to the result instance and used for display and
counting of significant results. The default is 0.01.
minSize:- An integer giving a minimum size for a gene
set for it to be tested. The default is 5.
testDirection:- A string indicating whether the test
should test for systematic increase (
"up") or decrease
("down") in the geneStats values within a gene set
relative to the remaining genes. graph:- The
graph
object indicating the hierarchical relationship among terms of the
ontology or other grouping.
conditional:- A
logical indicating whether
conditional tests should be performed. This tests whether a term
is still significant even when including its sub-terms in the model.
gsc:- The
GeneSetCollection
object grouping the gene ids into sets.
Methods
These are accessor methods for the various parameter slots:
- annotation<-
signature(object = "LinearMParams", value = "character"): ... - annotation
signature(object = "LinearMParams"): ... - categoryName
signature(r = "LinearMParams"): ... - conditional
signature(r = "LinearMParams"): ... - geneIds<-
signature(object = "LinearMParams"): ... - geneIds
signature(object = "LinearMParams"): ... - pvalueCutoff<-
signature(r = "LinearMParams"): ... - pvalueCutoff
signature(r = "LinearMParams"): ... - show
signature(object = "LinearMParams"): ... - testDirection<-
signature(r = "LinearMParams"): ... - testDirection
signature(r = "LinearMParams"): ... - conditional<-
signature(r = "LinearMParams"): ... - conditional
signature(r = "LinearMParams"): ... - universeGeneIds
signature(r = "LinearMParams"): ...
See Also
See linearMTest for
examples. ChrMapLinearMParams is a specialization
of this class for chromosome maps.