Man pages for sandraTL/PADIGM
Pathway Analysis with distance between genes and metablites

allShortestPaths-Graph-methodfunction that uses the object Graph and calculs distances for...
associatedShortestPaths-Graph-methodfunction that uses the object Graph and calculs distances for...
barplot_adjustMaximalDistancefunction to modify the frequency data.frame by adding more...
createGraphFromPathwaycreate df for vertices create df edges create graphEl objects...
createIGraph-GraphElements-methodCreation of object igraph with data from XML file of pathway...
distanceGeneToAllMetabolitefunction that output a barplot graph related to one specific...
finalReactionEdgeDFSince it is not possible to have the related gene when...
fromAssosDFEntryToIGraphIdDF-Graph-methodA igraph function
getCompoundNodeKgmlIdA igraph function
getDataFrameOfDuplicateCompoundsThis fucntion creates a data frame which contains the...
getDistanceAllFonction that calculates every shortest distances between...
getDistanceAssoFonction that calculates distance between each...
getFinalAssoDfSd-Graph-methodA igraph function
getFinalDFSHortestDistance-Graph-methodA igraph function
getHeadTailKgmlIdOfEdgeA igraph function
getIdGeneInGraph-Graph-methodA igraph function
getIdMetabolitesInGraph-Graph-methodA igraph function
getListEdgeFromGeneKGMLA KEGG Function
getListNodeFromKGMLThis function extract from KGML a list of metabolites (id and...
getListReactionFromKGMLA KEGGREST function
getPathwayKGMLA KEGG Function
Graph-classS4 classe Graph, contains all information important to create...
heatmapFunctionfunction that output a heatmap graph showing all results from...
helloHello, World!
igraph-classobject igraph instanciated as S4 classe to be able to use...
mergeRowsWithSmallestValueByKEGGIdmerge rows with smallest values in each col for repeated...
mergeVectorsLowerValuesfunction merge 2 numeric vectors and return a vector with the...
permutationFunctionPermutation test to evauluate if gene-metabolite associations...
removeRowsDistanceAllThsi function also sorts the data by metabolite or gene...
unlistEdgeReactionColFunction fractioning reaction list from every gene from KGML...
sandraTL/PADIGM documentation built on May 26, 2017, 12:27 a.m.