coexpression_enrichment: Calculate a Z score for enrichment for coexpression

In skinnider/flavin: A fast library for automated validation of interaction networks

Description

Calculate the enrichment among a set of interacting proteins for mRNA or protein co-expression, relative to a rewired version of the same network.

Usage

coexpression_enrichment(network, expr, bootstraps = 100, seed = 0,
  colname = "coexpr")

Arguments

network	a data frame containing interactions between protein pairs in the first two columns
expr	a matrix containing mRNA or protein expression data, with genes as columns
bootstraps	the number of times to rewire the network in order to calculate the Z score; defaults to 100
seed	the number to seed the rewiring algorithm with; defaults to zero
colname	the column name to assign to the shared annotations column created in the network data frame; defaults to "coexpr"

Value

a list with three objects: the median coexpression in the observed network; the median coexpression in each randomized network; and the Z score for the enrichment

skinnider/flavin documentation built on May 6, 2019, 10:49 a.m.