2.2 years ago by
United States
Hi,
Alternatively, you can use makeTxDbFromBiomart()
to make a TxDb object from the Ensembl Plants mart:
library(biomaRt)
mart <- useMart(biomart="plants_mart", host="plants.ensembl.org")
datasets <- listDatasets(mart)
datasets[1:6 , 1:2]
# dataset description
# 1 atauschii_eg_gene Aegilops tauschii genes (...
# 2 obrachyantha_eg_gene Oryza brachyantha genes (Oryza_brachya...
# 3 ptrichocarpa_eg_gene Populus trichocarpa gen...
# 4 ppersica_eg_gene Prunus persica genes...
# 5 stuberosum_eg_gene Solanum tuberosum genes (...
# 6 sitalica_eg_gene Setaria italica gene...
idx <- grep("oryza", datasets$description, ignore.case=TRUE)
datasets[idx, 1:2]
# dataset description
# 2 obrachyantha_eg_gene Oryza brachyantha genes (Oryza_br...
# 8 onivara_eg_gene Oryza nivara gene...
# 14 opunctata_eg_gene Oryza punctata gene...
# 15 oindica_eg_gene Oryza sativa Indica ...
# 18 oglumaepatula_eg_gene Oryza glumaepatula gene...
# 19 obarthii_eg_gene Oryza barthii gene...
# 20 osativa_eg_gene Oryza sativa Japonica g...
# 25 omeridionalis_eg_gene Oryza meridionalis genes (Oryza_me...
# 28 orufipogon_eg_gene Oryza rufipogon ...
# 38 olongistaminata_eg_gene Oryza longistaminata genes (O_long...
# 41 oglaberrima_eg_gene Oryza glaberrim...
Choose your dataset of interest (e.g. osativa_eg_gene
), then:
library(GenomicFeatures)
txdb <- makeTxDbFromBiomart(biomart="plants_mart",
dataset="osativa_eg_gene",
host="plants.ensembl.org")
Please note that some important tweaks were made to makeTxDbFromBiomart()
last week to improve its support for EnsemblGenomes (see here A: Errors with makeTxDbFromBiomart for the details) so make sure you use the latest version of GenomicFeatures (1.28.5) before trying the above.
Cheers,
H.
•
link
modified 2.2 years ago
•
written
2.2 years ago by
Hervé Pagès ♦♦ 14k