## ----style, echo = FALSE, results = 'asis', message=FALSE----------------
BiocStyle::markdown()

## ----bm------------------------------------------------------------------
tr <- "ENST00000373316"

## ----h38-----------------------------------------------------------------
suppressMessages(library("Gviz"))
suppressMessages(library("biomaRt"))

h38 <- useMart("ensembl", "hsapiens_gene_ensembl")
tr38 <- BiomartGeneRegionTrack(biomart = h38,
                               transcript = tr)
tr38 <- split(tr38, transcript(tr38))
tr38 <- ranges(tr38[[tr]])
tr38

## ----h37-----------------------------------------------------------------
h37 <- useMart(host = "feb2014.archive.ensembl.org",
                biomart = "ENSEMBL_MART_ENSEMBL",
                dataset = "hsapiens_gene_ensembl")
tr37 <- BiomartGeneRegionTrack(biomart = h37,
                               transcript = tr)
tr37 <- split(tr37, transcript(tr37))
tr37 <- ranges(tr37[[tr]])
tr37

## ----chain---------------------------------------------------------------
library("AnnotationHub")
hub <- AnnotationHub()
query(hub, 'hg19ToHg38')
chain <- query(hub, 'hg19ToHg38')[[1]]

## ------------------------------------------------------------------------
library("rtracklayer")
res <- liftOver(tr37, chain)
res <- unlist(res)

## set annotation
names(res) <- NULL
genome(res) <- "hsapiens_gene_ensembl"

all.equal(res, tr38)

## ----si------------------------------------------------------------------
sessionInfo()