manualChromPeaks {xcms} | R Documentation

## Manual peak integration and feature definition

### Description

The `manualChromPeaks` function allows to manually define chromatographic peaks which are added to the object's `chromPeaks` matrix. In contrast to `findChromPeaks()`, no peak detection is performed (e.g. using an algorithm such as centWave) but the peak is added as defined by the user. Note that a peak will not be added if no signal (intensity) was found in a sample within the provided boundaries.

Because chromatographic peaks are added to eventually previously identified peaks, it is suggested to run `refineChromPeaks()` with the `MergeNeighboringPeaksParam()` approach to merge potentially overlapping peaks.

The `manualFeatures` function allows to manually group identified chromatographic peaks into features by providing their index in the object's `chromPeaks` matrix.

### Usage

    manualChromPeaks(
      object,
      chromPeaks = matrix(),
      samples = seq_along(fileNames(object)),
      BPPARAM = bpparam(),
      msLevel = 1L
    )

    manualFeatures(object, peakIdx = list(), msLevel = 1L)

### Arguments

`object` | `XCMSnExp` or `OnDiskMSnExp` object.
`chromPeaks` | `matrix` defining the boundaries of the chromatographic peaks, one row per chromatographic peak, columns `"mzmin"`, `"mzmax"`, `"rtmin"` and `"rtmax"` defining the m/z and retention time region of each peak.
`samples` | optional `integer` to select samples in which the peak integration should be performed. By default performed in all samples.
`BPPARAM` | parallel processing settings (see `bpparam()` for details).
`msLevel` | `integer(1)` defining the MS level in which peak integration should be performed.
`peakIdx` | for `nabbyakFeatyres`: `list` of `integer` vectors with the indices of chromatographic peaks in the object's `chromPeaks` matrix that should be grouped into features.

### Value

`XCMSnExp` with the manually added chromatographic peaks or features.

### Author(s)

Johannes Rainer

[Package xcms version 3.16.1 Index]