wave128Window-methods: wave128Window generic

In sterlo/kineticWavelets: Small Library for Analysis of PacBio Kinetic Data using wavelets

Description

Reads a KineticWavelets object and creates wavelets for reads that match the DNAPattern

Usage

wave128Window(KineticWavelets, DNAPattern, ...)

## S4 method for signature 'KineticWavelets'
wave128Window(KineticWavelets, DNAPattern,
  maxReads = 1000, shiftWindow = 64, totalTime = TRUE, filterNumber = 1,
  shrink = 1)

Arguments

KineticWavelets	linkS4class{KineticWavelets} object
DNAPattern	The DNA pattern to search for in the reads
shiftWindow	The shift window determines where in the 128 bp window the element of interest lies. Default is 32 so that the element starts at base 33 in the window (i.e shifted from 1 by 32).
totalTime	If set te TRUE, they analysis will include the time spent on insert errors in the measurements. The default totalTime==FALSE results in an analysis in which the time spent on insert errors is not included.
filterNumber	The allows the filters number used in the wavelets transform to be adjusted. The default is filterNumber==1, the Haar wavelet transform.
shrink	The shrink options allows for only the upper quantiles to be examined. The default shrink==1 removes no data from the measurements. If shrink is set below 1, then only the values for the upper quantile above "shrink" are used (e.g shrink==0.05 returns the top 5 percent of the result). Measurements are shrunk at each scale of the wavelet coefficients.

Value

A list containining the kinetics for matched sequences

Author(s)

Sterling Sawaya [e-mail]

sterlo/kineticWavelets documentation built on May 30, 2019, 4:42 p.m.