Two-step centWave peak detection considering also isotopes — findChromPeaks-centWaveWithPredIsoROIs • xcms

This method performs a two-step centWave-based chromatographic peak detection: in a first centWave run peaks are identified for which then the location of their potential isotopes in the mz-retention time is predicted. A second centWave run is then performed on these regions of interest (ROIs). The final list of chromatographic peaks comprises all non-overlapping peaks from both centWave runs.

The CentWavePredIsoParam class allows to specify all settings for the two-step centWave-based peak detection considering also predicted isotopes of peaks identified in the first centWave run. Instances should be created with the CentWavePredIsoParam constructor. See also the documentation of the CentWaveParam for all methods and arguments this class inherits.

The findChromPeaks,OnDiskMSnExp,CentWavePredIsoParam method performs a two-step centWave-based chromatographic peak detection on all samples from an OnDiskMSnExp object. OnDiskMSnExp objects encapsule all experiment specific data and load the spectra data (mz and intensity values) on the fly from the original files applying also all eventual data manipulations.

snthreshIsoROIs,snthreshIsoROIs<-: getter and setter for the snthreshIsoROIs slot of the object.

maxCharge,maxCharge<-: getter and setter for the maxCharge slot of the object.

maxIso,maxIso<-: getter and setter for the maxIso slot of the object.

mzIntervalExtension,mzIntervalExtension<-: getter and setter for the mzIntervalExtension slot of the object.

polarity,polarity<-: getter and setter for the polarity slot of the object.

Usage

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

# S4 method for class 'OnDiskMSnExp,CentWavePredIsoParam'
findChromPeaks(
  object,
  param,
  BPPARAM = bpparam(),
  return.type = "XCMSnExp",
  msLevel = 1L,
  ...
)

# S4 method for class 'CentWavePredIsoParam'
snthreshIsoROIs(object)

# S4 method for class 'CentWavePredIsoParam'
snthreshIsoROIs(object) <- value

# S4 method for class 'CentWavePredIsoParam'
maxCharge(object)

# S4 method for class 'CentWavePredIsoParam'
maxCharge(object) <- value

# S4 method for class 'CentWavePredIsoParam'
maxIso(object)

# S4 method for class 'CentWavePredIsoParam'
maxIso(object) <- value

# S4 method for class 'CentWavePredIsoParam'
mzIntervalExtension(object)

# S4 method for class 'CentWavePredIsoParam'
mzIntervalExtension(object) <- value

# S4 method for class 'CentWavePredIsoParam'
polarity(object)

# S4 method for class 'CentWavePredIsoParam'
polarity(object) <- value

Arguments

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

numeric(1) defining the signal to noise ratio cutoff.

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.

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.

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.

object

For findChromPeaks: an OnDiskMSnExp object containing the MS- and all other experiment-relevant data.

For all other methods: a parameter object.

param

An CentWavePredIsoParam object with the settings for the chromatographic peak detection algorithm.

BPPARAM

A parameter class specifying if and how parallel processing should be performed. It defaults to bpparam. See documentation of the BiocParallel for more details. If parallel processing is enabled, peak detection is performed in parallel on several of the input samples.

return.type

Character specifying what type of object the method should return. Can be either "XCMSnExp" (default), "list" or "xcmsSet".

msLevel

integer(1) defining the MS level on which the peak detection should be performed. Defaults to msLevel = 1.

...

ignored.

value

The value for the slot.

Value

The CentWavePredIsoParam function returns a CentWavePredIsoParam class instance with all of the settings specified for the two-step centWave-based peak detection considering also isotopes.

For findChromPeaks: if return.type = "XCMSnExp" an XCMSnExp object with the results of the peak detection. If return.type = "list" a list of length equal to the number of samples with matrices specifying the identified peaks. If return.type = "xcmsSet" an xcmsSet object with the results of the peak detection.

Details

See centWave for details on the centWave method.

Parallel processing (one process per sample) is supported and can be configured either by the BPPARAM parameter or by globally defining the parallel processing mode using the register method from the BiocParallel package.

Slots

ppm,peakwidth,snthresh,prefilter,mzCenterFun,integrate,mzdiff,fitgauss,noise,verboseColumns,roiList,firstBaselineCheck,roiScales,extendLengthMSW,verboseBetaColumns,snthreshIsoROIs,maxCharge,maxIso,mzIntervalExtension,polarity: See corresponding parameter above.

Note

These methods and classes are part of the updated and modernized xcms user interface which will eventually replace the findPeaks methods. It supports chromatographic peak detection on OnDiskMSnExp objects (defined in the MSnbase package). All of the settings to the algorithm can be passed with a CentWavePredIsoParam object.

Author

Hendrik Treutler, Johannes Rainer

Examples


## Create a param object
p <- CentWavePredIsoParam(maxCharge = 4)
## Change snthresh parameter
snthresh(p) <- 25
p
#> Object of class:  CentWavePredIsoParam 
#>  Parameters:
#>  - snthreshIsoROIs: [1] 6.25
#>  - maxCharge: [1] 4
#>  - maxIso: [1] 5
#>  - mzIntervalExtension: [1] TRUE
#>  - polarity: [1] "unknown"
#>  - ppm: [1] 25
#>  - peakwidth: [1] 20 50
#>  - snthresh: [1] 25
#>  - prefilter: [1]   3 100
#>  - mzCenterFun: [1] "wMean"
#>  - integrate: [1] 1
#>  - mzdiff: [1] -0.001
#>  - fitgauss: [1] FALSE
#>  - noise: [1] 0
#>  - verboseColumns: [1] FALSE
#>  - roiList: list()
#>  - firstBaselineCheck: [1] TRUE
#>  - roiScales: numeric(0)
#>  - extendLengthMSW: [1] FALSE
#>  - verboseBetaColumns: [1] FALSE