Lift genome across builds

Source: R/utils.R

Lift genome across builds

liftover(gwas_data, build.conversion = "hg19.to.hg38", verbose = T)

Arguments

build_conversion

"hg19.to.hg38" (default) or "hg38.to.hg19.

See also

Other utils: ensembl_to_hgnc(), gather_files(), hgnc_to_ensembl()

Examples

data("BST1")
gr.lifted <- liftover(gwas_data=BST1, build.conversion="hg19.to.hg38")

#> [1] "XGR:: Lifting genome build: hg19.to.hg38"
#> Start at 2021-02-20 00:19:47
#> 
#> First, import the files formatted as 'GRanges' (2021-02-20 00:19:47) ...
#> 	import the data file (2021-02-20 00:19:47) ...
#> Second, construct GenomicRanges object (2021-02-20 00:19:47) ...
#> Third, lift intervals between genome builds 'hg19.to.hg38' (2021-02-20 00:19:47) ...
#> Start at 2021-02-20 00:19:47
#> 
#> 'chain' (from http://galahad.well.ox.ac.uk/bigdata/chain.RData) has been loaded into the working environment (at 2021-02-20 00:19:48)
#> 
#> End at 2021-02-20 00:19:48
#> Runtime in total is: 1 secs
#> 
#> End at 2021-02-20 00:19:48
#> Runtime in total is: 1 secs