computeDriverDistancePvalue: Compute Driver Distance P-Value

In Sage-Bionetworks/metanetwork: Network meta analysis

Compute Driver Distance P-Value

Description

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.

Sage-Bionetworks/metanetwork documentation built on April 27, 2022, 7:42 a.m.