associatedShortestPaths-Graph-method: function that uses the object Graph and calculs distances for...

In sandraTL/PADIGM: Pathway Analysis with distance between genes and metablites

Description

Note that for 1 gene is attached 1 enzyme which is an edge in our graph. In order to calcul a distance from vertice to vertice this function is called twice in function 'getFinalDFSHortestDistance'.

Usage

## S4 method for signature 'Graph'
associatedShortestPaths(object, data)

Arguments

object

Graph, data(mg, m, genes, metabolites)

Details

First call is to calcul all the distance for the one vertice of the gene to the all metabolites, the second call is to calcul the distance from the other vertice to all metabolites and then choose the smallest distance between the 2.

The selection of the first vertice and the second vertice is done in a other function 'getIdGeneInGraph'

param data where mg = id (from igraph in object Graph) of 1 metabolite related to the gene m = id (igraph in object Graph) genes = hsa:... id from KEGG metabolites = C.... id from KEGG

Examples

associatedShortestPaths(Graph, data)
calcul al distances
choosing smallest distance between the two metabolites of gene and
all metabolites

sandraTL/PADIGM documentation built on May 29, 2019, 1:45 p.m.