getFinalAssoDfSd-Graph-method: A igraph function

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

Description

Calls getIdGeneInGraph() twice to get : Modification of dataframe giving in entry by user, from c("gene", "metabolite") to 2 dataFrame where indexMetabolite = 1 d1 = c("metabolite1giIdIniGraph", "metabolitesIdIniGraph") #' where indexMetabolite = 2 d2 = c("metabolite2giIdIniGraph", "metabolitesIdIniGraph")

Usage

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

Arguments

graphe,

kegg id of compound of interest, dataframe of compounds (nodes)

Details

This is because genes are edges and we calculate vertex to vertex the distance between genes and metabolites. From each gene we want to take the shortest distance between the 2 vertex attached, so we calcul both and in an other function we take the smallest and that will be the output.

This function keeps, between the 2 metabolites of each gene vertexes, the distance that is the smallest between the 2 to the same metabolite.

Examples

getCompoundNodeKgmlId(g, data, indexMetabolite)

sandraTL/PathQuantPadigm documentation built on May 29, 2019, 1:46 p.m.