permutationTest: Statistical permutation test to asses the relevance of...

In sandraTL/PathQuant: Annotation of gene-metabolite pairs using topology of KEGG metabolic pathway maps

Description

Permutation test to evauluate if gene-metabolite associations are significantly closer than randomly selected gene-metabolite pairs.

Usage

permutationTest(pathwayId, association, gene, metabolite, permutation,
  output = c("medians", "pvalue", "histogram"))

Arguments

pathwayId	KEGG Id of selected pathway.
association	Dataframe with 2 columns, where each line reprensents an association. First column are genes and the sencond column are metabolites. Only use KEGG Ids.
gene	Dataframe of 1 column, representing all genes reported. Only use KEGG Ids.
metabolite	Dataframe of 1 column, representing all the measured metabolites. Only use KEGG Ids.
permutation	Number desired permutations
output	'medians' of all permutations, 'pvalue' of the permutation test, 'histogram' representing the distribution of all permutations' median

Details

If a gene or a metabolite is present on multiple edges or nodes, then the shortest distance is selected.

Examples

permutationFunction("hsa01100", shinAndAlDF,
            completeGeneDF,completeMetaboDF, 1000, "histogram")

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