liftOver: Lift intervals between genome builds
In rtracklayer: R interface to genome annotation files and the UCSC genome browser

Description Usage Arguments Value Author(s) References Examples

A reimplementation of the UCSC liftover tool for lifting features from one genome build to another. In our preliminary tests, it is significantly faster than the command line tool. Like the UCSC tool, a chain file is required input.

1	liftOver(x, chain, ...)

`x`	The intervals to lift-over, usually a `GRanges`.
`chain`	A `Chain` object, usually imported with `import.chain`, or something coercible to one.
`...`	Arguments for methods.

A GRangesList object. Each element contains the ranges mapped from the corresponding element in the input (may be one-to-many).

Michael Lawrence

http://genome.ucsc.edu/cgi-bin/hgLiftOver

## Not run: 
chain <- import.chain("hg19ToHg18.over.chain")
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
tx_hg19 <- transcripts(TxDb.Hsapiens.UCSC.hg19.knownGene)
tx_hg18 <- liftOver(tx_hg19, chain)

## End(Not run)