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

Description Usage Arguments Details Value Author(s) Examples

Description

Displays information on connected features of selected features.

Usage

1
2
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, thomasnaake@googlemail.com

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
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/MetCirc documentation built on May 8, 2019, 2:52 p.m.