CoHyperGParams-class {PCpheno} | R Documentation

## Class "CoHyperGParams"

### Description

A parameter class for representing all parameters needed for running the `hyperGTest` method with multiprotein complexes.

### Objects from the Class

Objects can be created by calls of the form `new("CoHyperGParams",...)`.

### Slots

`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.

`annotation`:

  A string giving the name of the annotation data package for the chip used to generate the data.

`cateogrySubsetIds`:

  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.

`categoryName`:

  A string describing the category. Usually set automatically by subclasses. For example "ScISI".

`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.

`testDirection`:

  A string indicating whether the test should be for overrepresentation (`"over"`) or underrepresentation (`"under"`).

### Methods

hyperGTest

  `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`

  Accessors for the gene identifiers that will be used as the selected gene list.

codeannotation(object)

  Accessor for annotation

`ontology(r)`

  Accessor for GO ontology.

`pvalueCutoff(r)`, `pvalueCutoff(r) <- value`

  Accessor for the p-value cutoff. When setting, `value` should be a numeric value between zero and one.

`testDirection`

  Accessor for the test direction. When setting, `value` must be either "over" or "under".

`universeGeneIds(r)`

  accessor for vector of gene identifiers.

`isConditional(r)`

  Returns `TRUE` if the instance has its conditional flag set

### Author(s)

S. Falcon and N. LeMeur

### See Also

`HyperGResult-class` `CoHyperGResult-class` `hyperGTest`

[Package PCpheno version 1.49.0 Index]