I'm looking to download the Wheat TILLING & SNP data from Ensembl from the biomaRt package in Bioconductor. However, I've noticed that the filters available in biomart website are more than what you have in the Bioconductor package. For e.g.
plantsDatabase <- useMart(biomart = 'plants_variations', host = 'plants.ensembl.org') plantsDatasets <- listDatasets(plantsDatabase) mainOrgIndex <- GetDatasetIndex(organism = mainOrganism,plantsDatasets$description) mainOrgDataset <- useDataset(mart = plantsDatabase,dataset = plantsDatasets$dataset[[mainOrgIndex]]) mainOrgFilters <- listFilters(mainOrgDataset) mainOrgAttributes <- listAttributes(mainOrgDataset) attributes=mainOrgAttributes$name[c(1:2,4:6,20:21,24,34:35)] filter=c('variation_source','variation_set_name','chr_name') values=list('EMS-induced mutation','EMS (Cadenza)','1A')
The GetDatasetIndex is a nifty function to fetch the index of the organism for which you are querying biomart, in this case 'Triticum aestivum'.
I wanted to filter the data by 'Variant consequence', filter available on biomart web portal but not in the biomaRt package (listFilters for this mart doesn't have this filter). Any pointers?