Function reference • dmfind

All functions

CCF(): Connected component fraction

NR(): Network Resampling

calc_X0_mean(): Calculate X0 mean

calc_adjND(): Calculation of permutation-adjusted network smoothing index

calc_dS(): Calculation of delta network smoothing indexes

calc_omega_i(): Calculation of omega i (internal)

calculate_ccf(): Calculate the connected component fraction

dS(): Delta Network Smoothing Index

dmfind_demo: Demo data

eval_eps(): Evaluate the effect of epsilon on NSI

extract_module(): Extraction and plotting of connected subnetworks from a graph and a set of selected vertices

find_sign_conn_comp(): Finding significant connected components

nsi(): Network Smoothing Index

omega(): Calculation of omega function

omega_perm(): Calculation of permuted omega function

plot_NR(): Plot the results of eval_eps

plot_NSI(): Scatter Plot of NSI values

plot_omega_eps(): Plot the results of eval_eps

string.v12.Entrez.ntm.700.400.k3: Interactome derived from STRING db v12.0 igraph object with 17288 genes and 174962 interactions. Only interactions with confidence >=700 and the top 3 interactions with confidence >=400 & < 700 were considered. Confidence score was calculated without textmining, as described at the URL https://string-db.org). Original protein identifiers were mapped to Entrez Gene identifiers using mappings from NCBI Entrez (https://ftp.ncbi.nlm.nih.gov dowload date 2023-09-19) and https://string-db.org