When I used local GREAT analysis with the function great(), following the description of great() as below figure show, I got an error.
res_posi <- great(ConstructGRanges(posi_ctg_data), "GO:MP", "mm10")
# error
* TSS source: TxDb.
* extended_tss is already cached, directly use it.
Error: Gene sets 'go:mp' is not supported.
However, if I changed "GO:MP" to "GO:MF", I got a result I wanted.
res_posi <- great(ConstructGRanges(posi_ctg_data), "GO:MF", "mm10")
* TSS source: TxDb.
* extended_tss is already cached, directly use it.
* use GO:MF ontology with 4967 gene sets (source: org.Mm.eg.db).
* check gene ID type in `gene_sets` and in `extended_tss`.
* use whole genome as background.
* remove excluded regions from background.
* overlap `gr` to background regions (based on midpoint).
* in total 953 `gr`.
* overlap extended TSS to background regions.
* check which genes are in the gene sets.
* only take gene sets with size >= 5.
* in total 2031 gene sets.
* overlap `gr` to every extended TSS.
* perform binomial test for each biological term.
hello jokergoo,
When I used local GREAT analysis with the function great(), following the description of great() as below figure show, I got an error.
However, if I changed "GO:MP" to "GO:MF", I got a result I wanted.
Is the description of function great() wrong?