SPUTNIK (version 1.1)

globalPeaksFilter: Reference similarity based peak selection.

Description

globalPeaksFilter returns a list of peaks selected by their similarity with a reference image.

Usage

globalPeaksFilter(msiData, referenceImage, method = "pearson",
  threshold = NULL, verbose = TRUE)

Arguments

msiData

msi.dataset-class object. See msiDataset.

referenceImage

ms.image-class object. Reference image used to calculate the similarity values.

method

method used to calculate the similariry between the peak intensities and the reference image. Accepted values are:

• pearson: Pearson's correlation

• spearman: Spearman's correlation

• ssim: structural similarity index measure

• nmi: normalized mutual information.

threshold

numeric (default = 0, default = 0.001 (SSIM)). The threshold applied to the similarity values between the peaks images and the reference image. The default value of 0 guarantees that only the ions with a positive similarity with the reference image (typically representing the spatial distribution of the signal source) are retrieved. For consistency, the NMI are scaled in [-1, 1] to match the same range of correlations.

verbose

logical (default = TRUE). Additional output text.

Value

peak.filter object. See linkapplyPeaksFilter.

Details

A filter based on the similarity between the peak signals and a reference signal. The reference signal, passed as an ms.image-class object, can be calculated using the refAndROIimages function. Both continuous and binary references can be passed. The filter then calculates the similarity between the peaks signal and the reference image and select those with a similarity larger than threshold. Multiple measures are available, correlation, structural similarity index measure (SSIM), and normalized mutual information (NMI). Since correlation can assume values in [-1, 1], also NMI are scaled in [-1, 1].

References

Wang, Z., Bovik, A. C., Sheikh, H. R., & Simoncelli, E. P. (2004). Image quality assessment: from error visibility to structural similarity. IEEE transactions on image processing, 13(4), 600-612.

Meyer, P. E. (2009). Infotheo: information-theoretic measures. R package. Version, 1(0).

See Also

countPixelsFilter applyPeaksFilter-msi.dataset-method

Examples

# NOT RUN {
## Load package
library("SPUTNIK")

## Mass spectrometry intensity matrix
X <- matrix(rnorm(200), 20, 40)

## Print original dimensions
print(dim(X))

## m/z vector
mzVector <- seq(600, 900, by = (900 - 600) / 39)

## Read the image size
imSize <- c(5, 4)

## Construct the ms.dataset object
msiX <- msiDataset(X, mzVector, imSize[1], imSize[2])

## Generate the reference image and the ROI mask
ref.roi <- refAndROIimages(msiX, refMethod = "sum", roiMethod = "otsu")

## Perform global peaks filter
glob.peaks <- globalPeaksFilter(msiData = msiX, referenceImage = ref.roi$Reference,
                                method = "pearson", threshold = 0)

## Apply the filter
msiX <- applyPeaksFilter(msiX, glob.peaks)

## Print the new dimensions
print(dim(getIntensityMat(msiX)))
# }