Multiple testing on the GO graph {globaltest}R Documentation

Multiple testing on the GO graph

Description

Three function 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

  gtGO(..., GO, focus, maxalpha = 0.05, stopafter = 100, verbose = FALSE)
  makeGOstructure(data, annotation, top, only.ids, ontology = c("BP", "CC", "MF"), unreliable)
  getFocus(GOstructure, maxatoms = 10)

Arguments

... Arguments describing the tests to be preformed are passed on to globaltest.
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.
data The data set for which the GOstructure object is to be made. Can be either an exprSet or a vector of probe indicators.
annotation The name of the metaData annotation package to be used.
top The node to be used as top node of the GOstructure. Defaults to one of "GO:0008150", "GO:0005575", "GO:0003674", depending on he ontology chosen. The GOstructure object will only contain offspring of the chosen top node.
only.ids A vector of GO ids. If this is supplied, GO ids not appearing in this list will not appear in the GOstructure object.
ontology The ontology to be used. One of Biological Process (BP), Cellular Component (CC) or Molecular Function (MF).
unreliable Can be used to designate one or more of the GO evidence codes as unreliable. Value must be a vector containing one or more from "IC", "IDA", "IEA", "IEP", "IGI", "IMP", "IPI", "ISS", "NAS", "ND", "RCA", "TAS", "NR".
GOstructure An object of class GOstructure.
maxatoms A tuning parameter that governs the choice of the focus level. getFocus will choose those GO terms in the focus level in such a way that all offspring gene sets of each focus level term can be constructed as unions of no more than maxatoms atom gene sets. Default value of maxatoms is 10. Higher values quickly lead to slower computation. Lower values typically lead to reduced power.

Details

These functions should be used in the following order. 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 gtGO 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

gtGO cannot be used in combination with the permutation version of globaltest.

Author(s)

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

References

For references, type: citation("globaltest"). See also the vignette GlobalTest.pdf included with this package.

See Also

Examples in the vignette! globaltest, GOstructure, gt.multtest.

Examples

    # Breast cancer data (exprSet) from the Netherlands Cancer
    # Institute with small GO structure (all descendants of Cell Cycle)
    # See the vignette for details on making a GO structure object.
    data(vandeVijver)
    data(gostructure.vandeVijver)

    focus <- getFocus(gostructure.vandeVijver)
    adjustedP <- gtGO(vandeVijver, "Surv(TIMEsurvival, EVENTdeath)",
      GO = gostructure.vandeVijver, focus = focus)

    # The significant GO graph can be visualized using
    # the GOstats and Rgraphviz packages.
    # See the vignette for details. Type: vignette("GlobalTest")

[Package globaltest version 4.4.0 Index]