data-raw/lad.R

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

# human.fibroblast.DamID.hg19.bed.txt: file containing LAD coordinates (Guelen et al., Nature, 2008) that was downloaded from
# http://compbio.med.harvard.edu/modencode/webpage/lad/human.fibroblast.DamID.hg19.bed

library(GenomicRanges)

lad.df <- read.table(file.path("/dcl01/scharpf1/data/dbruhm/delfi_followup/split-reads/pcawg_analysis/data/raw_data",
                               "human.fibroblast.DamID.hg19.bed.txt"))
lad <- GRanges(lad.df$V1, IRanges(lad.df$V2, lad.df$V3), score = lad.df$V4)
save(lad, file = "/dcl01/scharpf1/data/dbruhm/delfi_followup/split-reads/pcawg_analysis/data/processed_data/lad.rda")