Example of producing simple segmentation

segment_example.R

library(plyranges)
library(nullranges)

x <- data.frame(
  seqnames=rep(c("1","2","3"), each=10),
  start=rep(c(0:4, 10:14) * 1000 + 1, times=3),
  width=100) |>
  as_granges()

seqlengths(x) <- c("1"=20123, "2"=20123, "3"=20123)
isCircular(x) <- rep(FALSE,3)
genome(x) <- "abcd"
seqinfo(x)

# for real genomic data, tiles on the order of 1 Mb, and larger than block size
tiles <- tileGenome(seqlengths(x), tilewidth=5000, cut.last.tile.in.chrom=TRUE)

tiles <- tiles %>%
  mutate(num_olaps = count_overlaps(., x))

cut <- exp(mean(log(tiles$num_olaps+1)))

library(dplyr)
seg <- tiles |>
  mutate(state = case_when(
           num_olaps > cut ~ 1,
           num_olaps <= cut ~ 2))