createSimilarityMatrix: Create similarity matrix

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

Description

Creates the similarity matrix by calculating the normalised dot product (NDP) between precursors

Usage

createSimilarityMatrix(mm, m = 0.5, n = 2)

Arguments

mm	matrix, colnames are all fragments which occur in the dataset, rownames are m/z / rt values, entries of mm are intensity values corresponding to their m/z values
m	numeric, see ?NDP for further details
n	numeric, see ?NDP for further details

Details

createSimilarityMatrix calls a function to calculate the NDP between all precursors in the data set. For further information on how the NDP is calculated see ?NDP and Li et al. (2015): Navigating natural variation in herbivory-induced secondary metabolism in coyote tobacco populations using MS/MS structural analysis. PNAS, E4147–E4155. Currently m = 0.5 and n = 2 are set as default.

Value

createSimilarityMatrix returns a similarity matrix that contains the NDP similarity measure between all precursors in the data set

Author(s)

Thomas Naake, [e-mail]

Examples

data("binnedMSP", package = "MetCirc")
## truncate binnedMSP 
binnedMSP <- binnedMSP[1:28,]
createSimilarityMatrix(binnedMSP, m = 0.5, n = 2)

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