snMEGENA: SuperNOVA subgroup-specific hybrid MEGENA networks

In ryananeff/superNOVA: Differential coexpression within multiple subgroups of data

SuperNOVA subgroup-specific hybrid MEGENA networks

Description

Takes in an subgroup-specific hybrid correlation matrix from hybridCorMat and builds a MEGENA network from it.

Usage

snMEGENA(data.file, subtype.name, module.pval = 0.05, hub.pval = 0.05,
  cor.perm = 10, hub.perm = 50, n.cores = 1)

Arguments

data.file	Path to the hybrid correlation matrix.
subtype.name	Name of the subgroup for the output.
module.pval	Module significance p-value. Recommended is 0.05 (default).
hub.pval	Connectivity significance p-value based random tetrahedral networks. Recommended is 0.05 (default).
cor.perm	Number of permutations for calculating FDRs for all correlation pairs. Default is 10.
hub.perm	Number of permutations for calculating connectivity significance p-value. Default is 50.
n.cores	Number of cores to use with MEGENA. Default is 1 (single-threaded).
annot.table	Should we create an annotation table for the output? Default = TRUE.

Value

None (output to files)

ryananeff/superNOVA documentation built on March 29, 2024, 5:31 p.m.