printInformationSelect: Display information on connected features of selected...

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

Description

Displays information on connected features of selected features.

Usage

printInformationSelect(groupname, msp = NULL, ind, 
 lMatInd, linkMatrixThreshold, similarityMatrix, roundDigits = 2)

Arguments

groupname	character vector with groupname of selected feature, vector containing "group" and "name" to display, that is a unique identifier of the features, "group" and "name" have to be separated by "_" where "group" is the first and "name" is the last element
msp	MSP, an S4 object of class MSP for information about the selected feature
ind	numeric
lMatInd	numeric indices of selected features
linkMatrixThreshold	matrix that contains information of linked features for given thresholds
similarityMatrix	matrix that is used to get information on the degree of similarity, similarityMat is an ordered version of a similarity matrix, see ?createOrderedSimMat
roundDigits	numeric, how many digits should be displayed?

Details

printInformationSelect is for internal use.

Value

character that is in HTML format

Author(s)

Thomas Naake, [e-mail]

Examples

data("idMSMStoMSP", package = "MetCirc")
data("binnedMSP", package = "MetCirc")
## use only a selection
binnedMSP <- binnedMSP[c(1:20, 29:48, 113:132, 240:259),]
similarityMat <- createSimilarityMatrix(binnedMSP)
groupname <- rownames(similarityMat)
## order similarityMat according to mz
simMat <- createOrderedSimMat(similarityMat, order = "mz") 
groupnameMZ <- rownames(simMat)
linkMat_thr <- createLinkMatrix(simMat, 0.8, 1) 
ind <- 2
indMZ <- which(groupname[ind] == truncateName(groupnameMZ, NULL, group = TRUE))
linkMatInds <- getLinkMatrixIndices(groupnameMZ[indMZ], linkMat_thr)
MetCirc:::printInformationSelect(groupname = groupname, 
 msp = NULL, ind = ind, lMatInd = linkMatInds, 
 linkMatrixThreshold = linkMat_thr, 
 similarityMatrix = similarityMat, roundDigits = 2)

PlantDefenseMetabolism/MetabolomicTools documentation built on May 8, 2019, 2:53 p.m.