tabulate_windows: Tabulate the tetramers within a window advanced by step

In BigelowLab/tetramers: Tetramer Analysis with Principle Component Analysis

Tabulate the tetramers within a window advanced by step

Description

This generally is called with a DNAStringSet, and then is called recursively with DNAString.

Usage

tabulate_windows(x, tWindow = 1600, tStep = 200, tWidth = 4)

Arguments

x	a DNAStringSet (or DNAString)
tWindow	numeric, the width of the sliding window in base units
tStep	numeric, the number of bases to advance between successive window locations
tWidth	numeric, the width of the genome unit, for tetramer analysis it's 4

Value

for each DNAString a list of status (0/1 where 0 = ok) and x a tabulation matrix. In the matrix each row corresponds to a window location along the length of the sequence.

BigelowLab/tetramers documentation built on April 3, 2022, 8:22 p.m.