createLinkDf: Create a data frame which contains features to link (indices)

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

Description

Create a data frame which contains features to link (indices).

Usage

createLinkDf(similarityMatrix, spectra, condition, lower, upper)

Arguments

similarityMatrix	'matrix', a similarity matrix that contains the similarity measure between all precursors in the data set
spectra	MSpectra object containing spectra of similarityMatrix
condition	'character', vector containing the conditions/samples for which a linkDf is created
lower	'numeric', threshold value for similarity values, below this value linked features will not be included
upper	'numeric', threshold value for similarity values, above this value linked features will not be included

Details

'lower' and 'upper' are numerical values and truncate similar spectra. The function createLinkDf is a wrapper for the functions 'createLink0df' and 'thresholdLinkDf'.

Value

'createLinkDf' returns a data frame that gives per each row information on linked features

Author(s)

Thomas Naake, [e-mail]

Examples

data("spectra", package = "MetCirc")
data("similarityMat", package = "MetCirc")
link0df <- createLink0df(similarityMatrix = similarityMat,
    spectra_tissue, condition = c("SPL", "LIM", "ANT", "STY"))
createLinkDf(similarityMatrix = similarityMat, spectra = spectra_tissue,
    condition = c("SPL", "LIM", "ANT", "STY"), lower = 0.5, upper = 1)

MetCirc documentation built on Nov. 8, 2020, 8:26 p.m.