ddn3.pipeline

The convenience wrappers for running DDN

Module Contents

Functions

ddn_pipeline(dat1, dat2, gene_names[, lambda1, lambda2])

A wrapper around DDN
ddn3.pipeline.ddn_pipeline(dat1, dat2, gene_names, lambda1=0.3, lambda2=0.1)

A wrapper around DDN

Reads two data sets and a list of genes, then runs DDN and reports common and differential networks.

Parameters:

  • dat1 (array_like) – The first data for DDN

  • dat2 (array_like) – The second data for DDN

  • gene_names (list of str) – List of gene names for reporting and visualization

  • lambda1 (float, optional) – The parameter controlling the overall sparsity. Usually should be between 0 and 1

  • lambda2 (float, optional) – The parameter controlling the differences between two networks. Usually should be between 0 and 0.3

Returns:

  • comm_edge (pandas.DataFrame) – The common edges between the two networks

  • diff_edge (pandas.DataFrame) – The differential edges between the two networks

  • node_non_isolated (list of str) – List of nodes that have at least one neighboring nodes