植物构建txdb对象

使用genomicfeatures来构建txdb对象，首先就是安装对应的包

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

列出可用的数据库的

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

查找数据库中所有的植物的物种

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

下载数据

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

保存数据

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

载入

maize_txdb <- loadDb("maize_v4_2018_11.sqlite")