addSpectralSimilarity: Adding a spectral similarity matrix to the "structural"...

In tnaake/MetNet: Inferring metabolic networks from untargeted high-resolution mass spectrometry data

Adding a spectral similarity matrix to the "structural" 'AdjacencyMatrix'

Description

The function 'addSpectralSimilarity' adds adjacency matrices from spectral similarity into the "structural" 'AdjacencyMatrix' object. One or multiple spectral similarity matrices can be added to the "structural" 'AdjacencyMatrix' object.

Usage

addSpectralSimilarity(am_structural, ms2_similarity = list())

Arguments

am_structural	'AdjacencyMatrix' of type "structural" that was created using matching MS1 data of the same data set. The respective spectral similarity matrices will be added into 'am_structural'
ms2_similarity	'list' containing spectral similarity adjacency matrices with matching row-/colnames of the structural 'AdjacencyMatrix'. The name of the list entries should reference to the similarity calcululation method (e.g. "ndotproduct")

Details

The function 'addSpectralSimilarity' includes functionality to add spectral adjacency matrices e.g. that were created by functionality from the 'RforMassSpectrometry' infrastructure. 'addSpectralSimilarity' iterates through a 'list' with named spectral similarity matrices and adds them to the "structural" 'AdjacencyMatrix'. Matching between spectral similarity and "structural" 'AdjacencyMatrix' is performed via rownames/colnames. Thus, it is important that the spectral similarity matrices have row/colnames matching to the respective MS1 data. 'addSpectralSimilarity' will add the adjacency matrices and will return the "structural" 'AdjacencyMatrix' containing the added weighted adjacency matrices in the 'assays' slot.

Value

'AdjacencyMatrix' of type "structural" containing the respective adjacency matrices in the 'assay' slot as specified by 'methods'

Author(s)

Liesa Salzer, [e-mail]

Examples

data("x_test", package = "MetNet")
transformation <- rbind(
    c("Monosaccharide (-H2O)", "C6H10O5", "162.0528234315"),
    c("Disaccharide (-H2O)", "C12H20O11", "340.1005614851"),
    c("Trisaccharide (-H2O)", "C18H30O15", "486.1584702945"))
transformation <- data.frame(group = transformation[, 1],
    formula = transformation[, 2],
    mass = as.numeric(transformation[, 3]))
am_struct <- structural(x_test, transformation, var = c("group", "mass"),
    ppm = 10, directed = TRUE)

## load the file containing MS2 similarities
f <- system.file("spectra_matrix/spectra_matrix.RDS", package = "MetNet")
adj_spec <- readRDS(f)

## run the addSpectralSimilarity function
spect_adj <- addSpectralSimilarity(am_structural = am_struct,
   ms2_similarity = list("ndotproduct" = adj_spec))

tnaake/MetNet documentation built on Nov. 4, 2024, 4:45 a.m.