extract_seqs: Extract Pasted Sequences from Each Chromosome

In ShixiangWang/CNVMotif: Explore, Analyze and Visualize Catalogs and Patterns of Copy Number Variation in Cancer Genomics

Extract Pasted Sequences from Each Chromosome

Description

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

Usage

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.

Value

a list.

ShixiangWang/CNVMotif documentation built on June 3, 2022, 3:44 a.m.