nnMNF: Class nnMNF

In tofsims: Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data

Description

Class nnMNF contains methods for Maximum Autocorrelation Factors analysis

This method calculates MNF transform using an nearest neighbour estimate as implemented in mzImage from Stone et al. (2012).

Usage

nnMNF(dataObject, limitSNR = 1.5)

nnMNF(dataObject, limitSNR = 1.5)

Arguments

dataObject	object of type MassImage
limitSNR	numeric

Details

Class nnMNF contains methods for Maximum Autocorrelation Factors analysis

Minimum Noise Fraction according Green et al. (1988) but using a nearest neighbour estimate for the noise determination as seen in the package mzImage from Stone et al. (2012). As the mentioned package is no longer maintained, we used an archieved version as code base for a new version. The C code was implemented through Rcpp (Eddelbuettel and Francois, 2011). The present function is a user constructur that will create a new analysis slot in the chosen MassSpectra/MassImage object.

Value

object of class MNF

Examples

testImage<-MassImage('dummy')
testImage<-MNF(testImage)
image(analysis(testImage,1), comp = 1)
## Not run: 
library(tofsimsData)
data(tofsimsData)
testImage<-nnMNF(testImage)
image(analysis(testImage,1), comp = 1)
## End(Not run)

tofsims documentation built on Nov. 8, 2020, 5:10 p.m.