thresholdLinkMatrix: Threshold a link matrix

In PlantDefenseMetabolism/MetCirc: Navigating mass spectral similarity in high-resolution MS/MS metabolomics data

Description

Threshold a link matrix

Usage

thresholdLinkMatrix(linkMatrix, threshold_low, threshold_high)

Arguments

linkMatrix	matrix, a link matrix that gives per each row information on linked features
threshold_low	numeric, threshold value for NDP values, below this value linked features will not be returned
threshold_high	numeric, threshold value for NDP values, above this value linked features will not be returned

Details

threshold_low and threshold_high are numerical values and truncates similar/identical precursor ions; similarity is momentarily based on the normalised dot product.

Value

thresholdLinkMatrix returns a matrix that gives per each row information on linked features which are linked above a certain threshold

Author(s)

Thomas Naake, [e-mail]

Examples

data("binnedMSP", package = "MetCirc")
## use only a selection 
binnedMSP <- binnedMSP[c(c(1:20, 29:48, 113:132, 240:259)),]
similarityMat <- createSimilarityMatrix(binnedMSP)
linkMatrix <- createLink0Matrix(similarityMatrix = similarityMat)
thresholdLinkMatrix(linkMatrix = linkMatrix, 
     threshold_low = 0.5, threshold_high=1)

PlantDefenseMetabolism/MetCirc documentation built on May 8, 2019, 2:52 p.m.