REVIGO website update creating errors for DMRichR::REVIGO() and DMRichR::GOplot()
ben-laufer opened this issue · 1 comments
REVIGO has recently updated their website, which has temproarily broken DMRichR::REVIGO() and DMRichR::GOplot(). The fix for this isn't straightforward since their website now works very differently under the hood.
In order to prevent this issue from interfering with a DM.R run, some lines of code should be removed from DM.R: lines 655-662, 684-691, and 719-726. Additionally, the pipe operator %>% should be removed from lines: 654, 683, and 718.
I have contacted the developers of REVIGO and am hoping they will have some suggestions about how to access a mirror of their old site or see if it's possible to properly access the new one through R. If neither of those work out, I will implement a new method to slim GO terms (possibly the rrvgo package from Biocondcutor) in the next version of DMRichR, which should be released in the near future.
I've heard back from the REVIGO developers and the ability to use it in R again should be coming soon. However, I've implemented the rrvgo method in the developer branch. This branch can be downloaded through BiocManager::install("ben-laufer/DMRichR@dev").