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 3.8.0 Index]