centWaveP: CWT Based Chromatographic Peak Detection

Description Usage Arguments Details Value Attribution See Also

cent returns a list of all regions of interest as rectangles in m/z vs rt space.

1	cent(mz, i, scanindex, ppm = 2, prefilter = c(0, 0), maxskip = 0)

`mz`	numeric A vector of exact mass centroids, all scans concatenated.
`i`	numeric A vector of intensities corresponding to `mz`, all scans concatenated.
`scanindex`	integer A vector of integers corresponding to the start of a new scan in the `mz` and `i` vectors.
`ppm`	numeric the ppm mass error acceptable before a new ROI is initialized. This ppm is allowed on both sides of the mass.
`prefilter`	numeric a two integer vector. The first indicates the minimum number of peaks an ROI must contain to be retained. The second indicates the minimum intensity those muct be.
`maxskip`	integer The number of scans an ROI must not contain a peak before clossing the ROI. This is an addition to the original algorithm. Useful for QE data.

This function is a C++ implementation of the region of interest detection algorithm described in the centWave paper. The algorithm steps through scans sequentially and performs the following steps for every peak:

If there exists an ROI encompassing the mass, add the peak to that ROI.
If an appropriate ROI does not exist, create a new ROI.
Check all unfinished ROIs - if a peak hasn't been added within the previous maxskip scans save it.

A list, one entry for each region of interest.

This code was modified from the originally published centWave algorithm [1]. The code was orginally distributed and obtained under the GPL2 license via the xcms software package [2]. The original algorithms depend on the wavelet analysis code included in the MassSpecWavelet package [3]. All code herein was obtained under the GPL2 license and remains under the GPL 3 license or greater.

nathaniel-mahieu/centWaveP documentation built on May 23, 2019, 12:19 p.m.