## ----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)