I have generated KEGG tables from a differential methylation table many times before with the following code
annoEPIC <- getAnnotation(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) diffMethTable0.05 <- read.csv("diffMethTable_site_cmp9_0.05.csv", header = TRUE) tablep0.005 <- diffMethTable0.05[1:186,] sig.cpg0.005 <- as.character(tablep0.005[,2]) kegg <- gometh(sig.cpg = sig.cpg0.005, all.cpg = NULL, collection = "KEGG", array.type = "EPIC", plot.bias = TRUE)
However, during this past week I have been getting this error message, which I had never gotten before:
Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open URL 'http://rest.kegg.jp/list/pathway/Hsa': HTTP status was '400 Bad Request' sessionInfo( )
When I paste the URL that the error message mentions on Google, the page does not load. However, when I use the URL: https://rest.kegg.jp/list/pathway/hsa it does!
Has anyone else running gometh (with KEGG) been getting this message as well? How would I make gometh use the correct URL then?
I appreciate any help.
I am having the exact same problem. Any ideas anyone please?
I'm having the same issue. Not sure whats going on either.
I updated the packages that generate the KEGG tables (and also GO tables) and the tables were really different from what I had previously gotten with the other package version. Is this expected?