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

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

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

Description

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

Usage

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

Arguments

similarityMatrix	matrix, a similarity matrix that contains the similarity measure between all precursors in the data set
sps	Spectra object containing spectral data corresponding to features in similarityMatrix
condition	character vector containing the conditions/samples for which a linkDf is created
lower	numeric(1), threshold value for similarity values, linked features below this value will not be included
upper	numeric(1), threshold value for similarity values, linked features above this value will not be included

Details

lower and upper are numerical values and truncate spectra based on their similarity. 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,
    sps = sps_tissue, condition = c("SPL", "LIM", "ANT", "STY"))
createLinkDf(similarityMatrix = similarityMat, sps = sps_tissue,
    condition = c("SPL", "LIM", "ANT", "STY"), lower = 0.5, upper = 1)

tnaake/MetCirc documentation built on Nov. 3, 2024, 11:16 a.m.