refImageContinuous {SPUTNIK}

refImageContinuous returns the reference image, calculated using the method. This image represents the basic measure for the filters in SPUTNIK.

Description

refImageContinuous returns the reference image, calculated using the method. This image represents the basic measure for the filters in SPUTNIK.

Usage

refImageContinuous(
  msiData,
  method = "sum",
  mzQueryRef = numeric(),
  mzTolerance = Inf,
  useFullMZRef = TRUE,
  doSmooth = FALSE,
  smoothSigma = 2,
  alignTo = "detected",
  invertAligned = FALSE,
  verbose = TRUE
)

Arguments

msiData

msiDataset object..

method

string (default = "sum"). Method used to calculate the reference image. Valid values are:

• "sum": peak intensities sum

• "mean": average peak intensities (without zeros)

• "median": median peak intensities (without zeros)

• "pca": first principal component scores.

mzQueryRef

numeric. Mass-to-charge ratios used to calculate the reference image. Two values are interpreted as interval, multiple or single values are searched in the m/z vector. It overrides the useFullMZRef argument.

mzTolerance

numeric (default = Inf). Search window in parts-per-million units for the mzQueryRef.

useFullMZRef

logical (default = TRUE). Whether all peaks should be used to calculate the reference image. Ignored if mzQueryRef is provided.

doSmooth

logical (default = FALSE). If TRUE, the reference image is smoothed using a Gaussian kernel.

smoothSigma

numeric (default = 2). Standard deviation of the smoothing Gaussian kernel.

alignTo

string (default = "detected"). The reference image is aligned to the image representing:

• "detected": number of detected peaks

• "tic": total-ion-count image

The reference image will have a positive Pearson's correlation with the selected image.

invertAligned

logical (default = FALSE). If TRUE, the reference image has negative correlation with the selected image in alignTo.

verbose

logical (default = TRUE). Additional output text.

Details

Function to extract the continuous reference image from a msi.dataset-class object. The continuous reference image represents the spatial location of the sample. By default, it is aligned with either the image representing the number of detected peaks, or the total-ion-count in all pixels. It is expected to be higher in the region occupied by the sample (positive correlation with the mask representing the real sample pixels). In some cases, the alignment images can have higher values in the pixels outside of the sample. In these circumstances, the argument invertAligned should be set to TRUE.

Value

A continuous valued reference image (see msImage).

See Also

msiDataset, msImage

Examples

## Load package
library("SPUTNIK")

## Mass spectrometry intensity matrix
X <- matrix(rnorm(200), 20, 40)
X[X < 0] <- 0

## 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])

## Calculate the reference and ROI images from the ms.dataset-class object msiX.
## The reference is calculated as the first principal component scores scaled
## in [0, 1]; the binary ROI is calculated applying k-means on the entire dataset.
## Use only m/z values in the range of [700, 900]. The interval extremal values
## are matched within a tolerance of 50 ppm.

refImg <- refImageContinuous(msiX, method = "sum")
roiImg <- refImageBinaryOtsu(refImg)

## Plot the reference and region of interest ROI
## plot(ref.roi$Reference)
## plot(ref.roi$ROI)