cutLinkMatrix: Create a cut link matrix

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

Description

Create a cut link matrix

Usage

cutLinkMatrix(LinkMatrix, type = c("all", "inter", "intra"))

Arguments

LinkMatrix	matrix, that gives per each row information on linked features
type	character, one of "all", "inter" or "intra"

Details

This function is used to cut features from LinkMatrix. If type = "all", LinkMatrix will not be changed; if type = "inter" the cut LinkMatrix will only contain entries of links which are between groups and not inside groups; contrary to that, if type = "intra" the cut LinkMatrix will only contain entries of links which are inside groups and not between groups.

Value

cutLinkMatrix 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)
linkMat <- createLinkMatrix(similarityMatrix = similarityMat, threshold_low = 0.75, threshold_high = 1)
cutLinkMatrix(LinkMatrix = linkMat, type = "all")

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