liftOver {rtracklayer} | R Documentation

## Lift intervals between genome builds

### Description

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.

### Usage

    liftOver(x, chain, ...)

### Arguments

`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.

### Value

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

### Author(s)

Michael Lawrence

### References

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

### Examples

    ## 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)

[Package rtracklayer version 1.48.0 Index]