seq2nt: calculate local nucleotide content

In raim/segmenTools: Tools for Functional Genome Exploration

calculate local nucleotide content

Description

calculate local nucleotide content in moving windows and returns genomeData matrix TODO: move readFasta here and document!

Usage

seq2nt(
  seq,
  window = 100,
  step = 1,
  abc,
  skew = "",
  cum = FALSE,
  circular = FALSE,
  verb = FALSE
)

Arguments

seq	a sequence object as returned by readFasta
window	width of the moving window
step	step size
abc	sequence letters for which averages are calculated
skew	calculate skew for letters 1 and 2 in argument skew (e.g. skew=c("G","C"), skew=(G-C)/(G+C))
cum	set TRUE to calculate cumulative skew after Grigoriev 1998 NAR
circular	treat sequence as circular
verb	print progress messages

raim/segmenTools documentation built on April 25, 2024, 10:14 a.m.