GAKEGG (xx, ..., id, annotation, probe2entrez, multtest = c("holm", "BH", "BY"), sort = TRUE)
GAGO (xx, ..., id, annotation, probe2entrez, ontology = c("BP", "CC", "MF"), minsize=1, maxsize=Inf, multtest = c("holm", "focuslevel", "BH", "BY"), focuslevel = 10, sort = TRUE)
GABroad (xx, ..., id, annotation, probe2entrez, collection, category = c("c1", "c2", "c3", "c4", "c5"), multtest = c("holm", "BH", "BY"), sort = TRUE)
xx
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.probe2entrez
must be supplied.GAGO
also the focus level method is available.
See focusLevel
.TRUE
, sorts the results to increasing p-values.findFocus
is called with maxsize
at the specified level to find a focus level.getBroadSets
.annotate
and the appropriate annotation packages are installed.
GAKEGG
additionally requires the KEGG.db
package; GAGO
requires the
GO.db
package; GABroad
requires the user to download the XML file "msigdb_v2.5.xml"
from \ http://www.broad.mit.edu/gsea/downloads.jsp
, and to preprocess that file using
the getBroadSets
function.
gtGO
,
gtKEGG
,
gtBroad
,
GlobalAncova
,
gt
,
# see vignettes of packages GlobalAncova and globaltest and help of gtGO
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