This package consists of two MATLAB functions to assist users with
choosing the thresholds for wavelet denoising using the Cromwell
package.
[1]
function [smoothed, thresholds] = sizerPrep(inten, thresholds, infinity)
This function takes three inputs
inten = the raw spectrum intensities
thresholds = a vector of threshold settings to apply (default = 4:100)
infinity = a really large threshold setting (default = 1000)
The output consists of two objects
smoothed is a matrix containing the smooth spectra for all thresholds
thresholds is the vector of thresholds
The outputs can be used as inputs to the corresponding plotting routine,
sizerPlot.
[2]
function sizerPlot(spec, smoothed, thresholds, sml, range)
The inputs of this function are
spec = the raw intensity spectrum
smoothed = a matrix of smoothed spectra from sizerPrep
thresholds = a vector of thresholds from sizerPrep
sml = a vector of thresholds that should be displayed
range = a vector of spectrum time points to display
The function returns no outputs. Instead, it produces a graph containing a
heatmap of the deviations of the smooth spectra from the "infinitely
smoothed" spectrum, along with overlays of the raw spectrum and the smooths
corresponding to the minimal and maximal displayed thresholds.