Converts a list of MassPeaks objects into a matrix.
intensityMatrix(peaks, spectra)
peaks |
|
spectra |
|
peaks have to be binned by binPeaks before
calling intensityMatrix.
Returns a matrix containing intensities of all
MassPeaks objects of peaks and interpolated
intensity values for missing peaks if spectra was given or NA
otherwise.
The matrix has length(peaks) rows
(one row for each sample) and length(unique(mass)) columns.
There is an additional attribute "mass" that stores the mass values.
Sebastian Gibb mail@sebastiangibb.de
## load package
library("MALDIquant")
## create example MassPeaks objects
p <- list(createMassPeaks(mass=1:4,
intensity=11:14,
metaData=list(name="test mass peaks 1")),
createMassPeaks(mass=2:5,
intensity=22:25,
metaData=list(name="test mass peaks 2")))
## converts MassPeaks objects into a matrix
intensityMatrix(p)
## realistic example
## load example data
data("fiedler2009subset", package="MALDIquant")
## transform intensities
s <- transformIntensity(fiedler2009subset, method="sqrt")
## smoothing spectrum
s <- smoothIntensity(s, method="MovingAverage")
## remove baseline
s <- removeBaseline(s)
## call peak detection
p <- detectPeaks(s)
## bin peaks
p <- binPeaks(p)
## convert MassPeaks objects into a matrix with missing intensity
## values
intensityMatrix(p)
## convert MassPeaks and MassSpectrum objects into a matrix without
## missing intensity values
intensityMatrix(p, s)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.