data-raw/tad.R

In cancer-genomics/plasmasv: Methods for identification of tumor-specific structural variants in plasma

# IMR90_domains_hg19.bed.txt: file containing TAD coordinates in IMR90 cells (Dixon, Nature, 2012) that was downloaded from
# http://compbio.med.harvard.edu/modencode/webpage/hic/IMR90_domains_hg19.bed

library(GenomicRanges)

tad.df <- read.table("/dcl01/scharpf1/data/dbruhm/delfi_followup/split-reads/pcawg_analysis/data/raw_data/IMR90_domains_hg19.bed.txt")
tad.gr <- GRanges(seqnames = tad.df$V1, ranges = IRanges(start = tad.df$V2, end = tad.df$V3))
tad <- tad.gr

save(tad, file = "/dcl01/scharpf1/data/dbruhm/delfi_followup/split-reads/pcawg_analysis/data/processed_data/tad.rda")