msPeakInfo: Peak Detection Constructor Function
In zeehio/msProcess: Protein Mass Spectra Processing

Description Usage Arguments Value See Also Examples

Provides a common interface for packing detected mass spectrometry peaks into an appropriate output object.

1 2	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)