Hi, I am trying to use biomaRt to retrieve data for P. trichocarpa from phytozome. This is non standard, because the standard is via ensembl. However, the plant.ensembl.org database has V2.2 of poplar annotation and I would like to work with V3.0 (which is e.g. on phytozome)
I issue the following commands (adpted from what I used to do for retrieving data from ensembl), and obtain the following output:
host="phytozome.jgi.doe.gov" myset="phytozome" library(biomaRt) mylist<-listMarts(host=host) mysets<-listDatasets(useMart("phytozome_mart",host=host)) mydataset<-mysets$dataset[mysets$dataset==myset] allattributes<-listAttributes(useDataset(dataset = as.character(mydataset), mart = useMart("phytozome_mart",host = host))) #Use a given dataset for analysis myusemart <- useDataset(as.character(mydataset), mart = useMart("phytozome_mart", host = host)) resultTable <- getBM(attributes="organism_name", mart = myusemart) > allattributes[1:10,] name description 1 organism_name Organism Name 2 organism_id Proteome ID 3 gene_name1 Gene Name 4 gene_description Description 5 chr_name1 Chromosome Name 6 gene_chrom_strand Strand 7 gene_chrom_start Gene Start (bp) 8 gene_chrom_end Gene End (bp) 9 transcript_id PAC Transcript ID 10 transcript_name1 Transcript Name > resultTable organism_name 1 2 <html><head> 3
302 Found4 </head><body> 5
The document has moved https://phytozome.jgi.doe.gov/biomart/martservice?>here.7 </body></html>
So basically the list of the attributes is correctly defined, but when I try to do a query using the main querying function of biomaRt, I get that strange result, obviously meaning that there is something wrong. Did someone succeed in querying phytozome using biomaRt? Any help will be greatly appreciated!
Thank you very much. I am very happy with your patch!
I am attempting to use this solution, however, I get the following error when running the
I am using
biomaRt_2.44.4. I see that this error has already been reported to the Bioconductor user forum (several years ago). Should I post again? Thank you in advance for any help.
Yes, you should start a new thread on the Bioconductor support site with the code that generates the error and the output of