Inferring metabolic networks from untargeted high-resolution mass spectrometry data

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Documentation for package ‘MetNet’ version 1.23.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

MetNet-package	Inferring metabolic networks from untargeted high-resolution mass spectrometry data
.AdjacencyMatrix	Create S4 class AdjacencyMatrix
.assays_have_identical_colnames_rownames	Check if all the assays in the 'AdjacencyMatrix' object have identical colnames and rownames
.assays_have_identical_dimnames	Check if the assays in the 'AdjacencyMatrix' object have identical dimnames
addSpectralSimilarity	Adding a spectral similarity matrix to the "structural" 'AdjacencyMatrix'
addToList	Add adjacency matrix to list
AdjacencyMatrix	Wrapper to create an instance of S4 class AdjacencyMatrix
AdjacencyMatrix-class	Methods for 'AdjacencyMatrix' objects
AllGenerics	Placeholder for generics functions documentation
aracne	Create an adjacency matrix based on algorithm for the reconstruction of accurate cellular networks
as.data.frame	Methods for 'AdjacencyMatrix' objects
as.data.frame-method	Methods for 'AdjacencyMatrix' objects
bayes	Create an adjacency matrix based on score-based structure learning algorithm
clr	Create an adjacency matrix based on context likelihood or relatedness network
combine	Combine structural and statistical 'AdjacencyMatrix' objects
correlation	Create an adjacency matrix based on correlation
dim	Methods for 'AdjacencyMatrix' objects
dim-method	Methods for 'AdjacencyMatrix' objects
directed	Methods for 'AdjacencyMatrix' objects
directed-method	Methods for 'AdjacencyMatrix' objects
getLinks	Write an adjacency matrix to a 'data.frame'
lasso	Create an adjacency matrix based on LASSO
length-method	Methods for 'AdjacencyMatrix' objects
mat_test	Example data for 'MetNet': unit tests
mat_test_z	Example data for 'MetNet': unit tests
MetNet	Inferring metabolic networks from untargeted high-resolution mass spectrometry data
ms2_test	Spectra data to test addSpectralSimilarity
mz_summary	Create a summary from adjacency list containing mass differences
mz_vis	Visualize mass difference distribution
partialCorrelation	Calculate the partial correlation and p-values
peaklist	Example data for 'MetNet': data input
randomForest	Create an adjacency matrix based on random forest
rtCorrection	Correct connections in the structural adjacency matrices by retention time
show	Methods for 'AdjacencyMatrix' objects
show-method	Methods for 'AdjacencyMatrix' objects
spectra_matrix	Spectra data to test addSpectralSimilarity
sps_sub	Spectra data to test addSpectralSimilarity
statistical	Create an 'AdjacencyMatrix' object containing assays of adjacency matrices from statistical methods
structural	Create adjacency matrix based on m/z (molecular weight) difference
threshold	Threshold the statistical adjacency or spectral similarity matrices
thresholded	Methods for 'AdjacencyMatrix' objects
thresholded-method	Methods for 'AdjacencyMatrix' objects
topKnet	Return consensus ranks from a matrix containing ranks
type	Methods for 'AdjacencyMatrix' objects
type-method	Methods for 'AdjacencyMatrix' objects
x_annotation	Example annotation for 'MetNet': data input
x_test	Example data for 'MetNet': data input