createLinkMatrix: Create a matrix which contains features to link (indices)

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

Description

Create a matrix which contains features to link (indices)

Usage

createLinkMatrix(similarityMatrix, threshold_low, threshold_high)

Arguments

similarityMatrix	matrix, a similarity matrix that contains the NDP similarity measure between all precursors in the data set
threshold_low	numeric, threshold value for NDP values, below this value linked features will not be included
threshold_high	numeric, threshold value for NDP values, above this value linked features will not be included

Details

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

Value

createLinkMatrix returns a matrix that gives per each row information on linked features

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)
createLinkMatrix(similarityMatrix = similarityMat, 
     threshold_low = 0.5, threshold_high=1)

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