permutationFunction: Permutation test to evauluate if gene-metabolite associations...

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

Description

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

Usage

permutationFunction(pathwayId, data, geneMeasured, metaboliteMeasured,
  permutation, output = c("medians", "pvalue", "histogram"))

Arguments

data,

data.frame() colunm c(gene, metabolite) representing association between them for each row geneMeasured, list of evaluated genes in study (associated and not associated) metaboliteMeasured, list of measured metabolites in study (associated and not associated) permutation, number of permutation to execute output, "medians" median value of permutated sets - "pvalue" - "histogram"

Examples

permutationFunction("hsa01100", data, gene, metabolite, 1000)
take out chosen gene (and his number of reactions)
from list of possible genes
create new 'data' where associated genes and metabolites
are replace by shuffle genes and metabolites for genes

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