Cardinal (version 1.4.0)

reduceDimension-methods: Reduce the Dimension of an Imaging Dataset

Description

Apply dimension reduction to a mass spectrometry imaging dataset.

Usage

"reduceDimension"(object, method = c("bin", "resample"), ..., pixel = pixels(object), plot = FALSE)
"reduceDimension"(object, ref, method = "peaks", ...)
"reduceDimension"(object, ref, method = "peaks", ...)
## Bin the signal
reduceDimension.bin(x, t, width=200, offset=0, units=c("ppm","mz"), fun=sum, ...)
## Resample the signal
reduceDimension.resample(x, t, step=1, offset=0, ...)
## Reduce the signal to peaks
reduceDimension.peaks(x, t, peaklist, type=c("height", "area"), ...)

Arguments

object

An object of class MSImageSet.

ref

A reference to use to reduce the dimension, usually a peak list of m/z values or a peak-picked and aligned MSImageSet.

method

The method to use to reduce the dimensions of the signal.

pixel

The pixels to process. 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 dimension reduction method.

x

The mass spectrum to be reduced.

t

The corresponding m/z values.

width

The width of a bin.

step

The step size.

offset

Offset from the nearest integer.

units

Either parts-per-million or the raw m/z values.

fun

The function to be applied to each bin.

peaklist

A numeric vector giving the m/z values of the reference peaks.

type

Should the peak height or area under the curve be taken as the intensity value?

Value

An object of class MSImageSet with the dimension-reduced spectra.

Details

Dimension reduction 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: A numeric vector of intensities.
• t: A numeric vector of m/z values.
• tout: A numeric vector of m/z values to output.
• ...: Additional arguments.

The optional argument tout was added in version 1.3.1 to avoid cases where the output m/z values may be costly and inefficient to re-calculate for every spectrum.

A user-created function should return a list with two vectors of equal length, where the new length must be shorter than x and t:

• x: A numeric vector of new intensities.
• t: A numeric vector of new m/z values.

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

See Also

MSImageSet, peakPick, peakAlign, pixelApply

Examples

data <- generateImage(as="MSImageSet")
reduceDimension(data, method="resample", step=100, plot=interactive())