do_findChromPeaks_centWaveWithPredIsoROIs {xcms} | R Documentation

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

### Description

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
    )

    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.
`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.
`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"`.

### Details

For more details on the centWave algorithm see `centWave`.

### 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).

### Author(s)

Hendrik Treutler, Johannes Rainer

### See Also

Other core peak detection functions: `do_findChromPeaks_centWave()`, `do_findChromPeaks_massifquant()`, `do_findChromPeaks_matchedFilter()`, `do_findPeaks_MSW()`

[Package xcms version 3.16.1 Index]