Conversion of universe?

[AudreH]

Hello,
I'm using your package with the enrichGO function. The enrichment is done on Arabidopsis thaliana genes and TAIR identifers, with the org.At.tair.db package as reference.
I'm using it with the universe argument and I'm having trouble with the latest versions. Using it without the universe is fine. Using it with a universe leads to a message and a NULL result.
It seems the genes are converted to ENTREZID using bitr but if I'm not mistaken, the universe is not.
Once I use bitr on the universe, the function is working fine.
In the previous version, there was no issue with using a TAIR universe.

I'm on R-devel (4.6) and Bioconductor 3.23.

Here is an example:

genelist <- c("AT5G50600","AT4G28520","AT5G45690","AT1G54870","AT3G15670","AT2G42560","AT1G03890","AT4G36700","AT5G38170",
              "AT1G71695","AT3G05260","AT1G62290","AT3G21370","AT3G17520","AT2G33070","AT3G02480","AT1G21750","AT1G79690",
              "AT4G27140","AT5G54740","AT3G51810","AT4G21020","AT2G34700","AT1G48130")

universe <- c("AT5G50600","AT4G28520","AT5G45690","AT1G54870","AT3G15670","AT2G42560","AT1G03890","AT4G36700","AT5G38170",
              "AT1G71695","AT3G05260","AT1G62290","AT3G21370","AT3G17520","AT2G33070","AT3G02480","AT1G21750","AT1G79690",
              "AT4G27140","AT5G54740","AT3G51810","AT4G21020","AT2G34700","AT1G48130","AT2G33150","AT2G40170","AT5G58070",
              "AT1G07920","AT3G56350","AT1G56070","AT1G14940","AT5G01670","ATCG00490","AT1G16030","AT1G52690","AT3G21720",
              "AT1G77120","AT4G04460","AT4G39260","AT1G20620","AT3G23400","AT2G38380","AT3G58450","AT2G21820","AT5G40420",
              "AT5G57550","AT4G10020","AT3G21380","AT1G19900","AT5G03860","AT1G11910","AT1G01900","AT1G05510","AT5G46290",
              "AT3G53040","AT2G21660","AT5G06760","AT2G19900","AT3G57020","AT3G55440","AT3G22490","AT5G44120","AT5G14780",
              "AT5G44310","AT5G02240","AT1G14950","AT5G09810","AT2G07698","AT2G36640","AT1G72100","AT3G22500","AT2G05710",
              "AT4G25580","AT3G06050","AT3G15280","AT3G06860","AT4G20850","AT1G70840","AT5G07030","AT3G60730","AT1G54100",
              "AT5G50920","AT1G65090","AT1G79550","AT3G48990","AT4G13940","AT2G43520","AT2G01140","AT5G12030","AT1G11840",
              "AT2G18540","AT4G37870","AT2G17360","AT4G38740","AT1G19570","AT5G17310","AT5G13420","AT5G16970","AT1G24360",
              "AT5G09590","AT1G65930","AT3G52930","AT5G57655","AT1G04480","AT4G25140","AT4G36360","AT3G16640","AT5G52300",
              "AT5G66780","AT1G77510","AT5G20960","AT5G63030","AT2G36530","AT1G17100","AT1G57720","AT2G05990","AT5G20010",
              "AT1G73190","AT4G15530","AT4G09320","AT5G39720","AT3G54400","AT3G12490","AT1G22780","AT5G20290","AT5G52640",
              "AT2G15010","AT5G07190","AT2G36460","AT1G74310","AT4G16500","AT5G10160","AT3G17810","AT3G12580","AT3G62730")



## This one does not work
# returns: No gene sets have size between 1 and 500 ...
# --> return NULL...
yy <- enrichGO(genelist, OrgDb = 'org.At.tair.db', ont="BP",
               pvalueCutoff=1, qvalueCutoff = 1,
               universe = universe,
               minGSSize = 1,
               keyType = "TAIR")

## This one works fine
yy <- enrichGO(genelist, OrgDb = 'org.At.tair.db', ont="BP",
               pvalueCutoff=1, qvalueCutoff = 1,
               keyType = "TAIR")

## This one works fine
yy <- enrichGO(genelist, OrgDb = 'org.At.tair.db', ont="BP",
               pvalueCutoff=1, qvalueCutoff = 1,
               universe = bitr(universe,  fromType = "TAIR", toType = "ENTREZID", OrgDb = "org.At.tair.db")[["ENTREZID"]],
               keyType = "TAIR")

Thank you.

[guidohooiveld]

I can confirm that in the current release versions of R and Bioconductor (i.e. R-4.5.x and 3.22) the first example indeed works fine.
I suspect that the error is due to the fact that in the dev version functions to calculate enrichment have been moved to the package enrichit.

Pinging @GuangchuangYu to have a look at this; a fix may be easy to implement (it may be similar to this issue? #805).