Man pages for sandraTL/PathQuantPadigm
Pathway Analysis with distance between genes and metablites
| 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... |
