Core API function for two-step centWave peak detection with isotopes

The do_findChromPeaks_centWaveWithPredIsoROIs performs a two-step centWave based peak detection: chromatographic peaks are identified using centWave followed by a prediction of the location of the identified peaks' isotopes in the mz-retention time space. These locations are fed as regions of interest (ROIs) to a subsequent centWave run. All non overlapping peaks from these two peak detection runs are reported as the final list of identified peaks.

The do_findChromPeaks_centWaveAddPredIsoROIs performs centWave based peak detection based in regions of interest (ROIs) representing predicted isotopes for the peaks submitted with argument peaks.. The function returns a matrix with the identified peaks consisting of all input peaks and peaks representing predicted isotopes of these (if found by the centWave algorithm).

Usage

do_findChromPeaks_centWaveWithPredIsoROIs(
  mz,
  int,
  scantime,
  valsPerSpect,
  ppm = 25,
  peakwidth = c(20, 50),
  snthresh = 10,
  prefilter = c(3, 100),
  mzCenterFun = "wMean",
  integrate = 1,
  mzdiff = -0.001,
  fitgauss = FALSE,
  noise = 0,
  verboseColumns = FALSE,
  roiList = list(),
  firstBaselineCheck = TRUE,
  roiScales = NULL,
  snthreshIsoROIs = 6.25,
  maxCharge = 3,
  maxIso = 5,
  mzIntervalExtension = TRUE,
  polarity = "unknown",
  extendLengthMSW = FALSE,
  verboseBetaColumns = FALSE
)

do_findChromPeaks_addPredIsoROIs(
  mz,
  int,
  scantime,
  valsPerSpect,
  ppm = 25,
  peakwidth = c(20, 50),
  snthresh = 6.25,
  prefilter = c(3, 100),
  mzCenterFun = "wMean",
  integrate = 1,
  mzdiff = -0.001,
  fitgauss = FALSE,
  noise = 0,
  verboseColumns = FALSE,
  peaks. = NULL,
  maxCharge = 3,
  maxIso = 5,
  mzIntervalExtension = TRUE,
  polarity = "unknown"
)

Arguments

mz: Numeric vector with the individual m/z values from all scans/ spectra of one file/sample.
int: Numeric vector with the individual intensity values from all scans/spectra of one file/sample.
scantime: Numeric vector of length equal to the number of spectra/scans of the data representing the retention time of each scan.
valsPerSpect: Numeric vector with the number of values for each spectrum.
ppm: numeric(1) defining the maximal tolerated m/z deviation in consecutive scans in parts per million (ppm) for the initial ROI definition.
peakwidth: numeric(2) with the expected approximate peak width in chromatographic space. Given as a range (min, max) in seconds.
snthresh: For do_findChromPeaks_addPredIsoROIs: numeric(1) defining the signal to noise threshold for the centWave algorithm. For do_findChromPeaks_centWaveWithPredIsoROIs: numeric(1) defining the signal to noise threshold for the initial (first) centWave run.
prefilter: numeric(2): c(k, I) specifying the prefilter step for the first analysis step (ROI detection). Mass traces are only retained if they contain at least k peaks with intensity >= I.
mzCenterFun: Name of the function to calculate the m/z center of the chromatographic peak. Allowed are: "wMean": intensity weighted mean of the peak's m/z values, "mean": mean of the peak's m/z values, "apex": use the m/z value at the peak apex, "wMeanApex3": intensity weighted mean of the m/z value at the peak apex and the m/z values left and right of it and "meanApex3": mean of the m/z value of the peak apex and the m/z values left and right of it.
integrate: Integration method. For integrate = 1 peak limits are found through descent on the mexican hat filtered data, for integrate = 2 the descent is done on the real data. The latter method is more accurate but prone to noise, while the former is more robust, but less exact.
mzdiff: numeric(1) representing the minimum difference in m/z dimension required for peaks with overlapping retention times; can be negative to allow overlap. During peak post-processing, peaks defined to be overlapping are reduced to the one peak with the largest signal.
fitgauss: logical(1) whether or not a Gaussian should be fitted to each peak. This affects mostly the retention time position of the peak.
noise: numeric(1) allowing to set a minimum intensity required for centroids to be considered in the first analysis step (centroids with intensity < noise are omitted from ROI detection).
verboseColumns: logical(1) whether additional peak meta data columns should be returned.
roiList: An optional list of regions-of-interest (ROI) representing detected mass traces. If ROIs are submitted the first analysis step is omitted and chromatographic peak detection is performed on the submitted ROIs. Each ROI is expected to have the following elements specified: scmin (start scan index), scmax (end scan index), mzmin (minimum m/z), mzmax (maximum m/z), length (number of scans), intensity (summed intensity). Each ROI should be represented by a list of elements or a single row data.frame.
firstBaselineCheck: logical(1). If TRUE continuous data within regions of interest is checked to be above the first baseline. In detail, a first rough estimate of the noise is calculated and peak detection is performed only in regions in which multiple sequential signals are higher than this first estimated baseline/noise level.
roiScales: Optional numeric vector with length equal to roiList defining the scale for each region of interest in roiList that should be used for the centWave-wavelets.
snthreshIsoROIs: numeric(1) defining the signal to noise ratio cutoff to be used in the second centWave run to identify peaks for predicted isotope ROIs.
maxCharge: integer(1) defining the maximal isotope charge. Isotopes will be defined for charges 1:maxCharge.
maxIso: integer(1) defining the number of isotope peaks that should be predicted for each peak identified in the first centWave run.
mzIntervalExtension: logical(1) whether the mz range for the predicted isotope ROIs should be extended to increase detection of low intensity peaks.
polarity: character(1) specifying the polarity of the data. Currently not used, but has to be "positive", "negative" or "unknown" if provided.
extendLengthMSW: Option to force centWave to use all scales when running centWave rather than truncating with the EIC length. Uses the "open" method to extend the EIC to a integer base-2 length prior to being passed to convolve rather than the default "reflect" method. See https://github.com/sneumann/xcms/issues/445 for more information.
verboseBetaColumns: Option to calculate two additional metrics of peak quality via comparison to an idealized bell curve. Adds beta_cor and beta_snr to the chromPeaks output, corresponding to a Pearson correlation coefficient to a bell curve with several degrees of skew as well as an estimate of signal-to-noise using the residuals from the best-fitting bell curve. See https://github.com/sneumann/xcms/pull/685 and https://doi.org/10.1186/s12859-023-05533-4 for more information.
peaks.: A matrix or xcmsPeaks object such as one returned by a call to link{do_findChromPeaks_centWave} or link{findPeaks.centWave} (both with verboseColumns = TRUE) with the peaks for which isotopes should be predicted and used for an additional peak detectoin using the centWave method. Required columns are: "mz", "mzmin", "mzmax", "scmin", "scmax", "scale" and "into".

Value

A matrix, each row representing an identified chromatographic peak. All non-overlapping peaks identified in both centWave runs are reported. The matrix columns are:

mz: Intensity weighted mean of m/z values of the peaks across scans.
mzmin: Minimum m/z of the peaks.
mzmax: Maximum m/z of the peaks.
rt: Retention time of the peak's midpoint.
rtmin: Minimum retention time of the peak.
rtmax: Maximum retention time of the peak.
into: Integrated (original) intensity of the peak.
intb: Per-peak baseline corrected integrated peak intensity.
maxo: Maximum intensity of the peak.
sn: Signal to noise ratio, defined as (maxo - baseline)/sd, sd being the standard deviation of local chromatographic noise.
egauss: RMSE of Gaussian fit.

Additional columns for verboseColumns = TRUE:

mu: Gaussian parameter mu.
sigma: Gaussian parameter sigma.
h: Gaussian parameter h.
f: Region number of the m/z ROI where the peak was localized.
dppm: m/z deviation of mass trace across scans in ppm.
scale: Scale on which the peak was localized.
scpos: Peak position found by wavelet analysis (scan number).
scmin: Left peak limit found by wavelet analysis (scan number).
scmax: Right peak limit found by wavelet analysis (scan numer).

Additional columns for verboseBetaColumns = TRUE:

beta_cor: Correlation between an "ideal" bell curve and the raw data
beta_snr: Signal-to-noise residuals calculated from the beta_cor fit

Details

For more details on the centWave algorithm see centWave.

Author

Hendrik Treutler, Johannes Rainer

Usage

Arguments

Value

Details

See also

Author