SPUTNIK (version 1.1)

binSupervised,msi.dataset-method: Return a binary mask generated applying a supervised classifier on peaks intensities using manually selected regions corresponding to off-sample and sample-related areas.

Description

Return a binary mask generated applying a supervised classifier on peaks intensities using manually selected regions corresponding to off-sample and sample-related areas.

Usage

# S4 method for msi.dataset
binSupervised(object, refImage,
  mzQuery = numeric(), useFullMZ = T, mzTolerance = numeric(),
  method = "svm")

Arguments

object

msi.dataset-class object

refImage

ms.image-class object. Image used as reference to manually select the ROI pixels.

mzQuery

numeric. Values of m/z used to calculate the reference image. 2 values are interpreted as interval, multiple or single values are searched in the m/z vector. It should be left unset when using useFullMZRef = TRUE.

useFullMZ

logical (default = TRUE). Whether all the peaks should be used to calculate the reference image.

mzTolerance

numeric. Tolerance in PPM to match the mzQueryRef values in the m/z vector. Only valid when useFullMZ = FALSE.

method

string (default = 'svm'). Supervised classifier used to segment the ROI.

Value

ms.image-class object representing the binary mask image.