topGOresult-class {topGO} | R Documentation

## Class "topGOresult"

### Description

Class instance created by `getSigGroups-methods` or by `runTest`

### Objects from the Class

Objects can be created by calls of the form `new("topGOresult", description, score, testName, algorithm, geneData)`.

### Slots

`description`:

  character string containing a short description on how the object was build.

`score`:

  named numerical vector containing the p-values or the scores of the tested GO terms.

`testName`:

  character string containing the name of the test statistic used.

`algorithm`:

  character string containing the name of the algorithm used.

`geneData`:

  list containing summary statistics on the genes/gene universe/annotations.

### Methods

`score`:

  method to access the `score` slot.

`testName`:

  method to access the `testName` slot.

`algorithm`:

  method to access the `algorithm` slot.

`geneData`:

  method to access the `geneData` slot.

`show`:

  method to print the object.

`combineResults`:

  method to aggregate two or more topGOresult objects. `method = c("gmean", "mean", "median", "min", "max")` provides the way the object scores (which most of the time are p-values) are combined.

.

### Author(s)

Adrian Alexa

### See Also

`groupStats-class`, `getSigGroups-methods`

### Examples

    data(results.tGO)

    s <- score(resultFisher)

    go <- sort(names(s))
    go.sub<- sample(go, 100)
    go.mixed <- c(sample(go, 50), sample(ls(GOCCTerm), 20))
    go.others <- sample(ls(GOCCTerm), 100)

    str(go)
    str(go.sub)
    str(go.mixed)
    str(go.others)

    str(score(resultFisher, whichGO = go))
    str(score(resultFisher, whichGO = go.sub))
    str(score(resultFisher, whichGO = go.mixed))
    str(score(resultFisher, whichGO = go.others))

    avgResult <- combineResults(resultFisher, resultKS)
    avgResult
    combineResults(resultFisher, resultKS, method = "min")

[Package topGO version 2.39.1 Index]