Multiple testing on the GO graph {GlobalAncova} | R Documentation

## Multiple testing on the GO graph

### Description

Three functions adapted from package globaltest to test (part of) the GO graph for association of the gene expression profile of GO terms with a response variable. Used together, these functions return multiplicity-adjusted p-values calculated using the Focus Level procedure that preserves the structure of the GO graph.

### Usage

      GAGO(..., GO, focus, maxalpha = 0.05, stopafter = 100, verbose = FALSE)

### Arguments

`...` | Arguments describing the tests to be performed are passed on to `GlobalAncova`. Note that only the approximative version of `GlobalAncova` is used here and hence the parameter `method` is not available. Even though the number of permutations (`perm`) may be specified since very large gene sets (with more genes than `max.group.size`) are treated with the permutation test.
`GO` | An object of class `GOstructure` describing the structure of the GO graph. This object should be created using `makeGOstructure`.
`focus` | A vector of GO ids to describe te focus level. Typically made using `getFocus`.
`maxalpha` | The maximum multiplicity-adjusted p-value. The algorithm will stop when this value is exceeded.
`stopafter` | The maximum number of significant GO terms to be found. The algorithm will stop when this value is exceeded.
`verbose` | If set to `TRUE`, prints much more extensive progress information.

### Details

Previous to a call to `GAGO`, first use `makeGOstructure` to make a GO graph tailored to a specific data set. Then `getFocus` can be used to choose a focus level. Finally `GAGO` performs the focus level procedure.

### Value

The function returns a named vector of multiplicity-adjusted p-values. Adjusted p-values of GO terms not appearing in this vector are larger than the chosen value of `maxalpha`.

### Note

Function `GAGO` corresponds to function `gtGO` in package globaltest. The difference is in the use of the `GlobalAncova` test instead of `globaltest` within the focus level procedure.

### Author(s)

Jelle Goeman: j.j.goeman@lumc.nl; Jan Oosting; Manuela Hummel

### References

Goeman, J.J. and Mansmann, U., Family-wise error rate on the directed acyclic graph of Gene Ontology, submitted.

### See Also

`gtGO`, `GlobalAncova`, `globaltest`, `GOstructure`, `makeGOstructure`, `getFocus`

### Examples

      # see vignettes of packages GlobalAncova and globaltest and help of gtGO

[Package GlobalAncova version 3.4.0 Index]