## ----echo=FALSE, results="hide", warning=FALSE--------------------------------
suppressPackageStartupMessages({
library('liftOver')
})

## ----doit,echo=FALSE,results="hide"-------------------------------------------
library(gwascat)
library(GenomicRanges)
library(rtracklayer)
library(Homo.sapiens)
library(BiocGenerics)
library(liftOver)

## ----lkOne,eval=FALSE---------------------------------------------------------
#  library(gwascat)
#  cur = makeCurrentGwascat()  # result varies by day

## ----lkcur--------------------------------------------------------------------
data(cur)
cur

## ----getch--------------------------------------------------------------------
library(rtracklayer)
path = system.file(package="liftOver", "extdata", "hg38ToHg19.over.chain")
ch = import.chain(path)
ch
str(ch[[1]])

## ----dolift-------------------------------------------------------------------
seqlevelsStyle(cur) = "UCSC"  # necessary
cur19 = liftOver(cur, ch)
class(cur19)

## ----ul-----------------------------------------------------------------------
cur19 = unlist(cur19)
genome(cur19) = "hg19"
cur19 = new("gwaswloc", cur19)
cur19

## ----lkloss-------------------------------------------------------------------
length(cur)-length(cur19)
setdiff(mcols(cur)$SNPS, mcols(cur19)$SNPS)