Compute Driver Distance P-Value

Calculates the Driver Distance of `geneSet` in `graph` as described in `metanetworks::computeDriverDistance` and permutes `nsamp` permutations of random gene sets from `graph` which are the size of `geneSet` to create a null distribution to derive p-values for the Driver Distances of `geneSet`.

Usage

computeDriverDistancePvalue(geneSet, graph, nsamp = 100)

Arguments

geneSet

Required. A user specified gene set corresponding to vertex names in `graph`. All the names are not required to be entirely represented in the graph object.

graph

Required. An igraph graph object consisting of vertices of genes and edges representing co-expression between genes.

nsamp

Optional. Number of permutations to build null distribution for p-value construction (Default = 100)

Value

a list consisting of a mean distance of genes within the largest component to each other, the pairwise list of distances, and a vector the length of `nsamp` consisting of the null distribution to calculate the p-value.