Function reference • edgynode

Plot functions

Comparative visualisation of network inference outcomes.

Summary functions

Summarise network inference outcomes.

summary_centrality_alpha(): Find Bonacich alpha centrality scores of network positions

summary_centrality_harmonic(): Harmonic centrality of vertices

summary_centrality_kleinberg(): Kleinberg's hub and authority centrality scores.

summary_centrality_subgraph(): Find subgraph centrality scores of network positions

summary_delta_con_similarity(): Calculate DeltaCon similarity

Helpers

is_adjacency(): Check whether a matrix fulfills the edgynode adjacency matrix convention

is_binary(): Check if a numeric matrix generated with make_adjacency and make_binary is binary

is_standard(): Check if a numeric matrix generated with make_adjacency fulfills the edgynode standard format

is_symmetric(): Check if a make_adjacency converted matrix is symmetric

make_adjacency(): Convert a raw input matrix into an edgynode adjacency matrix

make_binary(): Convert a numeric matrix generated with make_adjacency into a binary matrix

make_standard(): Force a numeric matrix generated with make_adjacency into the edgynode standard matrix format

make_symmetric(): Force a matrix into being symmetric

import_genie3(): Output Parser for GENIE3

ppcor(): Output Parser for PPCOR

assert_adjacency(): Check whether a matrix fulfills the edgynode adjacency matrix convention

convert_adj_to_edges(): Convert an adjacency matrix to an edge list

convert_adj_to_igraph(): Convert an adjacency matrix to igraph object

convert_adj_to_matrix(): Convert an adjacency matrix to plain matrix

convert_edges_to_adj(): Convert an edge list to an adjacency matrix

metric_dist_delta_con(): Calculate graph distance based on DeltaCon

network_benchmark_noise_filtering(): Benchmarking of noise filtering and normalization impact on network inference

network_benchmark_noise_filtering_test(): Perform a statistical test on noise filter benchmarking results

network_dist_pairwise_genes(): Comparison of binary adjacency weights of the same gene in two different networks

network_filter_edges(): Matrix filter edges

network_make_binary(): Matrix convert to binary

network_rescale(): Rescaling function customized for adjacency matrices