Valley detection and centroidization
Checks envelopes calculated by envelope for valleys and extracts centroids or intensoids.
vdetect(profiles,detect="centroid",plotit=TRUE,verbose=TRUE)
profiles |
List of stick profiles as generated by |
detect |
To return either |
plotit |
Should results be plotted, |
verbose |
Verbose, |
List with length equal to length of list profiles, with equal names of list entries.
Each entry in that list contains the centroids, intensoids or valleys of the envelope in two columns:
m/z |
m/z |
abundance |
Area (centroid) or abundance (intensoid, valley) |
Valley: local profile minimum, i.e. any envelope stick flanked by two other sticks of higher abundance.
Stick: see envelope.
Centroid mass: intensity-weighted sum of the m/z of sticks between two valleys.
Centroid intensity: profile area between two valleys (mean of upper and lower sum of stick intensities), normalized to the maximum centroid area of the envelope.
Intensoid mass: m/z of the most intense stick between two valleys.
Intensoid intensity: intensity of the most intensive stick between two valleys, normalized to the most intense intensoid.
Too low stick discretization leads to imprecision in valley, centroid and intensoid characteristics.
Martin Loos, Christian Gerber
############################
# batch of chemforms #######
data(isotopes)
data(chemforms)
chemforms<-chemforms[1:5]
pattern<-isopattern(
isotopes,
chemforms,
threshold=0.1,
plotit=TRUE,
charge=FALSE,
emass=0.00054858,
algo=2
)
profiles<-envelope(
pattern,
ppm=FALSE,
dmz=0.0001,
frac=1/4,
env="Gaussian",
resolution=1E6,
plotit=TRUE
)
centro<-vdetect(
profiles,
detect="centroid",
plotit=TRUE
)
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