hg19轉(zhuǎn)hg38
my_liftover <- function(peaks,from_to = 'hg19_hg38'){
if(from_to == 'hg19_hg38') {
path <- '/mdshare/node8/txmdata/scATAC_seq/AtacAnnoR/data/genome_files/hg19ToHg38.over.chain'
ch <- rtracklayer::import.chain(path)
one_liftover <- function(peak){Signac::GRangesToString(rtracklayer::liftOver(Signac::StringToGRanges(peak), ch)[[1]][1])}
# one_liftover('chr19-44821468-44827058')
if(length(peaks) > 1000){
out_peaks <- pbmcapply::pbmclapply(peaks,one_liftover,mc.cores = 10) %>% unlist()
} else{
out_peaks <- lapply(peaks,one_liftover) %>% unlist()
}
}
return(out_peaks)
# which(hg38_peaks == '--')
}
peaks <- c('chr19-44821468-44827058','chr1-44821468-44827058')
my_liftover(peaks)
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