# Inferring metabolic networks from untargeted high-resolution mass spectrometry data

## Documentation for package ‘MetNet’ version 1.16.0

- 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