generate_individual_graphs: Builds graphs from specified network layers

In molnet-org/molnet: Predicting Differential Drug Response using Multi-Omics Networks

Description

Constructs and returns two graphs for each network layer, where nodes correspond to the rows in the measurement data. Graphs are initially complete and edges are weighted by correlation of measurements across columns. The number of edges is then reduced by either a threshold on the p-value of the correlation or a minimum scale-free fit index. Each node is mapped to the biological identifiers given in the layer and the mapping table is returned as 'annotations'.

Usage

generate_individual_graphs(layers, settings)

Arguments

layers	Named list with different network layers containing data and identifiers for both groups (generated from make_layer)
settings	A named list containing pipeline settings

Value

A nested named list with first-level elements 'graphs' and 'annotations'. The second level elements are 'group1' and 'group2'. These contain a list of iGraph objects ('graphs') and data frames ('annotations') mapping the graph node IDs to biological identifiers.

Examples

data(layers_example)
layers <- layers_example
settings <- molnet::molnet_settings(handling_missing_data="pairwise.complete.obs")
individual_graphs <- molnet::generate_individual_graphs(layers, settings)
molnet::graph_metrics(individual_graphs$graphs$group1$mrna)
molnet::graph_metrics(individual_graphs$graphs$group2$mrna)

molnet-org/molnet documentation built on Dec. 21, 2021, 8:59 p.m.