生信常用脚本

1.用自己的gtf文件构建txdb数据结构，用于下游分析(The TxDb class is a container for storing transcript annotations)

library(GenomicFeatures)
#gtf、gff  to txdb
makeTxDbFromGFF()
#other way
makeTxDbFromGRanges
makeTxDbFromUCSC
makeTxDbFromBiomart
makeTxDbFromEnsembl
####ref(http://lutgw1.lunet.edu/usr/lib64/R/library/GenomicFeatures/html/TxDb-class.html)

2.提取transcripts、exons、genes、promoters and so on

library(GenomicFeatures)
#x is A TxDb object.
transcripts(x, ...)
exons(x, ...)
genes(x, ...)
promoters(x, upstream=2000, downstream=200, ...)
###ref(http://lutgw1.lunet.edu/usr/lib64/R/library/GenomicFeatures/html/transcripts.html)