R/examples/filter_split.R

In SPUTNIK: SPatially aUTomatic deNoising for Ims toolKit

## 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, 601, by = (601 - 600) / 39)

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

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

## Determine split peaks
sp.filter <- splitPeaksFilter(
  msiData = msiX, mzTolerance = 50,
  sharedPixelsRatio = 0,
  sparseness = "spatial.chaos", threshold = 0.5
)