Multiple testing on the GO graph {GlobalAncova} | R Documentation |
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.
GAGO(..., GO, focus, maxalpha = 0.05, stopafter = 100, verbose = FALSE)
... |
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. |
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.
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
.
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.
Jelle Goeman: j.j.goeman@lumc.nl; Jan Oosting; Manuela Hummel
Goeman, J.J. and Mansmann, U., Family-wise error rate on the directed acyclic graph of Gene Ontology, submitted.
gtGO
, GlobalAncova
, globaltest
,
GOstructure
, makeGOstructure
, getFocus
# see vignettes of packages GlobalAncova and globaltest and help of gtGO