使用genomicfeatures來構(gòu)建txdb對(duì)象，首先就是安裝對(duì)應(yīng)的包

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GenomicFeatures", version = "3.8")
BiocManager::install("biomaRt", version = "3.8")
library("GenomicFeatures")
library("biomaRt")

列出可用的數(shù)據(jù)庫的

listMarts()
listMarts(host = "http://plants.ensembl.org")

查找數(shù)據(jù)庫中所有的植物的物種

mart<-useMart(biomart = "plants_mart",host = "http://plants.ensembl.org")
datasets <- listDatasets(mart)
datasets$dataset

下載數(shù)據(jù)

maize_txdb<-makeTxDbFromBiomart(biomart = "plants_mart",dataset = "zmays_eg_gene",host = "http://plants.ensembl.org")

保存數(shù)據(jù)

saveDb(maize_txdb, file="maize_v4_2018_11.sqlite")

載入

maize_txdb <- loadDb("maize_v4_2018_11.sqlite")