seq2nt: calculate local nucleotide content

Description Usage Arguments

View source: R/seqTools.R

Description

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

Usage

1
2
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 abc (e.g. abc=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 Nov. 9, 2018, 5:38 p.m.