peakAlign-methods {Cardinal} | R Documentation

## Peak Align an Imaging Dataset

### Description

Apply peak alignment to a mass spectrometry imaging dataset.

### Usage

    ## S4 method for signature 'MSImageSet,numeric'
    peakAlign(object, ref, method = c("diff", "DP"),
        ...,
        pixel = pixels(object),
        plot = FALSE)

    ## S4 method for signature 'MSImageSet,MSImageSet'
    peakAlign(object, ref, ...)

    ## S4 method for signature 'MSImageSet,missing'
    peakAlign(object, ref, ...)

    ## Absolute difference alignment
    peakAlign.diff(x, y, diff.max=200, units=c("ppm", "mz"), ...)

    ## Dynamic programming alignment
    peakAlign.DP(x, y, gap=0, ...)

### Arguments

`object` | An object of class `MSImageSet`.
`ref` | A reference to which to align the peaks.
`method` | The peak alignment method to use.
`pixel` | The pixels to align. If less than the extent of the dataset, this will result in a subset of the data being processed.
`plot` | Plot the mass spectrum for each pixel while it is being processed?
`...` | Additional arguments passed to the peak alignment method.
`x` | The vector of m/z values to be aligned.
`y` | The vector of reference m/z values.
`diff.max` | Peaks that differ less than this value will be aligned together.
`units` | Either parts-per-million or the raw m/z values.
`gap` | The gap penalty for the dynamic programming sequence alignment.

### Details

If a `MSImageSet` object is used as the reference then the local maxima in its mean spectrum will be calculated and used as the reference m/z values. The method looks for a “mean” column in the object's `featureData`, and if it does not exist, then the mean spectrum will be calculated using `featureApply(ref, mean)`. If the reference is missing, the method will use the object itself as the reference.

Peak alignment is usually performed using the provided functions, but a user-created function can also be passed to `method`. In this case it should take the following arguments:

- `x`: The vector of m/z values to be aligned.

- `y`: The vector of reference m/z values.

- `...`: Additional arguments.

A user-created function should return a vector of the same length as `x` and `y` where `NA` values indicate no match, and non-missing values give the index of the matched peak in the reference set.

Internally, `pixelApply` is used to apply the peak alignment. See its documentation page for more details on additional objects available to the environment installed to the peak alignment function.

### Value

An object of class `MSImageSet` with the peak aligned spectra.

### Author(s)

Kylie A. Bemis

### See Also

`MSImageSet`, `peakPick`, `peakFilter`, `reduceDimension`, `pixelApply`

### Examples

    data <- generateImage(diag(2), as="MSImageSet")
    peaks <- peakPick(data, method="simple", plot=interactive())
    peaks <- peakAlign(peaks, data, method="diff", plot=interactive())

[Package Cardinal version 1.12.1 Index]