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... |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.