refImageBinaryKmeans: Calculate the binary reference image using k-means...

In SPUTNIK: Spatially Automatic Denoising for Imaging Mass Spectrometry Toolkit

Calculate the binary reference image using k-means clustering. K-Means is run on the first 'npcs' principal components to speed up the calculations.

Description

Calculate the binary reference image using k-means clustering. K-Means is run on the first 'npcs' principal components to speed up the calculations.

Usage

refImageBinaryKmeans(
  dataset,
  npcs = 10,
  alignTo = "detected",
  invertAligned = FALSE
)

Arguments

dataset	msi.dataset-class object. See msiDataset.
npcs	int (default = 10). Number of principal components to calculate.
alignTo	string (default = "detected"). Sample reference image to align the estimate binary image. It is expected to correlate with the sample location.
invertAligned	boolean (default = FALSE). If TRUE, the binary image is inverted after being aligned to the sample reference (alignTo).

Value

ms.image-class object with binary intensities.

SPUTNIK documentation built on May 29, 2024, 11:53 a.m.