msPeakInfo {msProcess} | R Documentation |
Provides a common interface for packing detected mass spectrometry peaks into an appropriate output object.
msPeakInfo(x, y, index.min, index.max, noise.local = NULL, snr.thresh = 2)
x |
A numeric vector representing the m/z values of a spectrum. |
y |
A numeric vector representing the intensity values of the spectrum. |
index.max |
A logical vector the size of the original mass spectrum. If the
kth element is TRUE , it indicates that the corresonding kth element of the
original mass spectrum is a local maxima. |
index.min |
A logical vector the size of the original mass spectrum. If the
kth element is TRUE , it indicates that the corresonding kth element of the
original mass spectrum is a local minima. It is assumed that for each peak (identified
as a TRUE element in index.max ) there exists two minima which encompass
the peak in time. Hence, it is expected that length(which(index.min)) will be one
greater than length(which(index.max)) . |
noise.local |
A numeric vector representing the estimated instantaneous noise level,
i.e., one noise element for each m/z value. This argument is used to form signal-to-noise
ratio (SNR) estimates that are subsequently compared to the snr.thresh argument in the
pruning process. Default: NULL (no SNR pruning is performed). |
snr.thresh |
A numeric value representing the signal intensity threshold.
Only the local maxima whose signal intensity is above this value
will be recorded as peaks. Default: 2 . |
A data.frame with 10 columns: peak class location, left bound, right bound and
peak span in both clock tick
("tick.loc"
, "tick.left"
, "tick.right"
, "tick.span"
)
and mass measure
("mass.loc"
, "mass.left"
, "mass.right"
, "mass.span"
),
and peak signal-to-noise ratio and intensity
("snr"
, "intensity"
).
Since noise.local
is NULL
, "snr"
is the same as ("intensity"
).
msPeak
, msPeakSimple
, msPeakMRD
, msPeakCWT
.
if (!exists("qcset")) data("qcset", package="msProcess") ## create faux MS peak data z <- qcset[seq(500), 1] x <- z$mz y <- z$intensity noise <- as.vector(wavCWT(y, n.scale=1)) index.min <- peaks(-y, span=31) index.max <- peaks(y, span=31) ## pack data using the constructor msPeakInfo(x, y, index.min, index.max, noise.local=noise, snr.thresh=1.3)