allShortestPaths-Graph-method | function that uses the object Graph and calculs distances for... |
associatedShortestPaths-Graph-method | function that uses the object Graph and calculs distances for... |
barplot_adjustMaximalDistance | function to modify the frequency data.frame by adding more... |
createGraphFromPathway | create df for vertices create df edges create graphEl objects... |
createIGraph-GraphElements-method | Creation of object igraph with data from XML file of pathway... |
distanceGeneToAllMetabolite | function that output a barplot graph related to one specific... |
finalReactionEdgeDF | Since it is not possible to have the related gene when... |
fromAssosDFEntryToIGraphIdDF-Graph-method | A igraph function |
getCompoundNodeKgmlId | A igraph function |
getDataFrameOfDuplicateCompounds | This fucntion creates a data frame which contains the... |
getDistanceAll | Fonction that calculates every shortest distances between... |
getDistanceAsso | Fonction that calculates distance between each... |
getFinalAssoDfSd-Graph-method | A igraph function |
getFinalDFSHortestDistance-Graph-method | A igraph function |
getHeadTailKgmlIdOfEdge | A igraph function |
getIdGeneInGraph-Graph-method | A igraph function |
getIdMetabolitesInGraph-Graph-method | A igraph function |
getListEdgeFromGeneKGML | A KEGG Function |
getListNodeFromKGML | This function extract from KGML a list of metabolites (id and... |
getListReactionFromKGML | A KEGGREST function |
getPathwayKGML | A KEGG Function |
Graph-class | S4 classe Graph, contains all information important to create... |
heatmapFunction | function that output a heatmap graph showing all results from... |
hello | Hello, World! |
igraph-class | object igraph instanciated as S4 classe to be able to use... |
mergeRowsWithSmallestValueByKEGGId | merge rows with smallest values in each col for repeated... |
mergeVectorsLowerValues | function merge 2 numeric vectors and return a vector with the... |
permutationFunction | Permutation test to evauluate if gene-metabolite associations... |
removeRowsDistanceAll | Thsi function also sorts the data by metabolite or gene... |
unlistEdgeReactionCol | Function fractioning reaction list from every gene from KGML... |
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