Extract Pasted Sequences from Each Chromosome

See get_score_matrix() for examples. The result sequences are unique and sorted.

extract_seqs(
  dt,
  len = 5L,
  step = 1L,
  local_cutoff = 1e+07,
  flexible_approach = FALSE,
  return_dt = FALSE
)

Arguments

dt	a `data.table` from transform_seqs.
len	cut length.
step	step size to move on each chromosome sequence.
local_cutoff	any segment with length greater than this cutoff will be filtered out and used as cutpoint, default is `10Mb`.
flexible_approach	if `TRUE`, extract flexible-size sequences between segments with size less than specified cutoff. So the arguments `len` and `step` are ignored.
return_dt	if `TRUE`, just return a `data.table` containing mutated `Seqs` column.

a list.