library(ggtut)
example(g17rngsnr)
ranges(g17rngsnr)
library(illuminaHumanv1.db)
get("GI_21237796-A", illuminaHumanv1CHRLOC)
library(rtracklayer)
ch = import.chain("/Users/stvjc/Bioconductor/Docs/Papers/RangesPaper/hg18ToHg19.over.chain")
gg = liftOver(g17rngsnr, ch)
gg
ggg = unlist(gg)
ggg
names(ggg) = mcols(ggg)[,1]
ggg
names(mcols(ggg)) = "probeid"
ggg
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
seqinfo(ggg) = seqinfo(TxDb.Hsapiens.UCSC.hg19.knownGene)
seqinfo(ggg) = seqinfo(TxDb.Hsapiens.UCSC.hg19.knownGene)[paste0("chr", 1:22)]
seqlevels(ggg)
seqinfo(ggg) = seqinfo(TxDb.Hsapiens.UCSC.hg19.knownGene)["chr17"]
ggg
ls()
g17rngsnr = ggg
save(g17rngsnr, file="g17rngsnr.rda")
data(CPS17)
CPS17
data(package="ggtut")
data(snpgr17)
snpgr17
data(g17rngsnr)
g17rngsnr
ls()
g17rngsnr
dir()
load("g17rngsnr.rda")
getwd()
setwd("ggtut/data")
getwd()
load("g17rngsnr.rda")
g17rngsnr
dir()
snpgr17
sss = liftOver(snpgr17, ch)
sss2 = unlist(sss)
sss2
seqlevels(sss2)
sss2
sss
snpgr17
mcols(snpgr17)$rsid = names(snpgr17)
snpgr17
sss = liftOver(snpgr17, ch)
sss
sss2 = unlist(sss)
genome(sss2)
genome(sss2) = "hg19"
sss2
sss2[which(seqnames(sss2)!="chr17")]
sss2
snpgr17 = sss2
save(snpgr17, file="snpgr17.rda")
savehistory(file="addrfixes.hist.txt")
