PeakFilling: Peak filling of any missed peaks

In speaq2: Wavelet Based Tools for Feature-Wise Analysis and Quantification of Nuclear Magnetic Resonance (NMR) Spectra

Description

This functions detects which samples (after alignment) are missing from every aligned peak group and reanalyses the raw data to verify whether this peak is actually non-existent for this sample

Usage

PeakFilling(Y.aligned, Y.spec, max.index.shift = 10, window.width = "small",
  nCPU = -1)

Arguments

Y.aligned	Aligned peaks (after the 'PeakAligner' function).
Y.spec	The raw NMR spectra in matrix format.
max.index.shift	Maximal shift in index between a filled peak and the group it belongs to.
window.width	The width of the detection window for the wavelets. Because of the Fourier transform lengths of 512 ( window.width = 'small') of 1024 ( window.width = 'large') are preferable.
nCPU	The amount of cpu's to be used for peak detection. If set to '-1' all available cores minus 1 will be used.

Value

Returns a data frame with aligned peaks and possibly extra peaks obtained from the raw data (these peaks have SNR = NA).

Author(s)

Charlie Beirnaert, [e-mail]

Examples

## Not run: 
# This function works on a data frame resulting from the 'PeakAligner' function 
# DetectedPeaks <- getWaveletPeaks(X.ppm= PPM.vector, Y=Y.spec,  baselineThresh = 10,nCPU  = 4)
# Aligned.peaks = PeakAligner = function (Y.peaks = DetectedPeaks)
Filled.Peaks = SpecPeak.filling(Y.aligned = Aligned.peaks, Y.spec = Y)

## End(Not run)

speaq2 documentation built on May 6, 2017, 4:09 a.m.