concub-class {geecc} | R Documentation

## Class `"concub"`

### Description

An object of type concub

### Details

Specifying the background population is crucial for the tests for association between factors. Usually the population is the set of all probe sets represented on a micro-array or the set of all genes in a genome. If an expression set is passed with the population-parameter, all probe sets beginning with the pattern “AFFX” (Affymetrix quality control) are removed.

### Objects from the Class

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

### Slots

`categories`:

  A named list of named lists. Each item of the outer list represents the two or three categories. Each item of the inner lists represents a variable of the category.

`population`:

  A character vector containig the background population. As an alternative, an object with class ‘eSet’, ‘ExpressionSet’, or ‘DGEList’; background population is then set to the outcome of `rownames(population)`.

`keep.empty.vars`:

  A boolean list with names being names of `categories`.

`options`:

  Additional options for individual categories. See Details.

`approx`:

  specifies the minimum expected value when an exact hypergeometric test (below) or the chi-squared approximation should be used. Defaults to 0.

`null.model`:

  A formula specifying the null-model of the test.

`test.result`:

  A list to store test results. Filled up after `runConCub`.

`test.result.filter`:

  A list to store filtered test results. Filled up after `filterConCub`.

`test.result.filter.heatmap`:

  A list to store heatmaps for further manipulation. Filled up after `plotConCub`.

The last three slots are not set by the user.

### Methods

getTable

  `signature(object = "concub")`: creates a table containing the results of the tests.

  Usage: `getTable(object, na.rm=TRUE, dontshow=list())`

  Arguments:

  object

    an object of type concub

  na.rm

    logical. If `TRUE` (the default), rows with `NA` P-values (or odds ratios) are removed

  The resulting table is a data frame with 8 or 10 columns, depending on if a two- or three-way test was applied

  1. 'factor1':this column has the name of the first category

  2. 'factor2':this column has the name of the second category

  3. 'factor3':this column has the name of the third category

  4. n.'factor1':number of items in variable of first category

  5. n.'factor2':number of items in variable of second category

  6. n.'factor3':number of items in variable of third category

  7. p.value:(probably adjusted) p-value

  8. log2.odds.ratio:log2 of the sample odds ratio

  9. n.tags:number of items at position x_{1,1,1} or x_{1,1}

  10. tags:items at position x_{1,1,1} or x_{1,1} (e.g. gene identifiers)

  You have to run `filterConCub()` before you can get the table. If `filterConCub()` was not run, a warning is shown and `getTable` returns `NULL`.

show

  `signature(object = "concub")`

### See Also

`GOStats` to perform a simple two-way enrichment analysis

### Examples

    showClass("concub")

[Package geecc version 1.20.0 Index]