Entering edit mode
Sebastien Gerega
▴
370
@sebastien-gerega-2229
Last seen 10.0 years ago
Hi,
I would like to identify overrepresented GO in my dataset using the
topGO package.
I am working with a C. neoformans oligo array and have the GO
annotation
in a list with the following format:
$`162.m02116`
[1] GO:0009536
4026 Levels: GO:0 GO:00 GO:000 GO:0000 GO:00000 GO:000000 GO:0000001
GO:0000002 GO:0000004 GO:0000006 GO:0000009 GO:0000010 ... GO:0051861
$`162.m02150`
[1] GO:0009536
4026 Levels: GO:0 GO:00 GO:000 GO:0000 GO:00000 GO:000000 GO:0000001
GO:0000002 GO:0000004 GO:0000006 GO:0000009 GO:0000010 ... GO:0051861
$`162.m02156`
[1] GO:0005554 GO:0008372 GO:0000004
4026 Levels: GO:0 GO:00 GO:000 GO:0000 GO:00000 GO:000000 GO:0000001
GO:0000002 GO:0000004 GO:0000006 GO:0000009 GO:0000010 ... GO:0051861
How do I go about creating the GOdata object?
GOdata = new("topGOdata",
ontology = "MF",
allGenes = selectedList,
annot = annFUN.GO2genes, ## the new annotation function
GO2genes = myGO2genes) ## the GO to gene ID's dataset
Specifically what do I use for the annotation function? It is unclear
to
me how to write this aspect.
Am I correct in understanding that I supply my list as the final
argument?
thanks,
Sebastien