I'm trying to access Cyanobase through BiomaRt, but failing:
library(biomaRt) cyanobase <- useMart("cyanobase_1",dataset="Synechocystis") Checking attributes ... ok Checking filters ... ok > attributes <- listAttributes(cyanobase) # this shows me there is an attribute called "CDS" for example. > getBM(attribute=("CDS"), mart = cyanobase) Error in getBM(attribute = ("CDS"), mart = cyanobase) : Invalid attribute(s): CDS Please use the function 'listAttributes' to get valid attribute names
I have checked the attributes list and CDS is there but I don't know why the getBM function fails to find it. I tried changing the dataset to another cyanobacteria and it still fails, I've also tried other attributes, but no luck. I also tried the human example using ensemble in the biomaRt manual and this works fine. When I change to cyanobase, it fails with this error. Any ideas? Thanks.