| 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 |