SilhouetR: SilhouetR

In speaq: Tools for Nuclear Magnetic Resonance (NMR) Spectra Alignment, Peak Based Processing, Quantitative Analysis and Visualizations

SilhouetR

Description

This function calculate Silhouette values. The function is generic, as such silhouette values can be calculated between samples of different classes or it can be used to calculate silhouette values between different groups of peaks. This is the way in which it is used for the speaq package (see the example).

Usage

SilhouetR(DataMatrix, GroupIndices, distance = "euclidean")

Arguments

DataMatrix	a matrix with the raw data, 1 variable per column.
GroupIndices	The vector with the group indices (length must be equal to the amount of rows in DataMatrix).
distance	The distance metric to be used, "euclidean" or "manhattan".

Value

Returns the silhouette values. Note if a group contains only 1 no Silhouette value can be calculated (will give NA)

Author(s)

Charlie Beirnaert, [e-mail]

Examples

subset <- GetWinedata.subset()
# to reduce the example time we only select spectra 1 & 2
subset.spectra = as.matrix(subset$Spectra)[1:2,] 
subset.ppm = as.numeric(subset$PPM)

test.peaks <- getWaveletPeaks(Y.spec=subset.spectra, 
                              X.ppm=subset.ppm,
                              nCPU = 1) # nCPU set to 2 for the vignette build
                              
test.grouped <- PeakGrouper(Y.peaks = test.peaks)

Silhouette.values = SilhouetR(DataMatrix = test.grouped$peakPPM, 
                              test.grouped$peakIndex, 
                              distance = "euclidean")
                              
hist(Silhouette.values$SilhouetteValues)

speaq documentation built on May 23, 2022, 5:06 p.m.