reduceDimension-methods {Cardinal} | R Documentation |
Apply dimension reduction to a mass spectrometry imaging dataset.
## S4 method for signature 'MSImageSet,missing' reduceDimension(object, method = c("bin", "resample"), ..., pixel = pixels(object), plot = FALSE) ## S4 method for signature 'MSImageSet,numeric' reduceDimension(object, ref, method = "peaks", ...) ## S4 method for signature 'MSImageSet,MSImageSet' 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"), ...)
object |
An object of class |
ref |
A reference to use to reduce the dimension, usually a peak list of m/z values or a peak-picked and aligned |
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 |
type |
Should the peak height or area under the curve be taken as the intensity value? |
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.
An object of class MSImageSet
with the dimension-reduced spectra.
Kylie A. Bemis
MSImageSet
,
peakPick
,
peakAlign
,
pixelApply
data <- generateImage(as="MSImageSet") reduceDimension(data, method="resample", step=100, plot=interactive())