BRCA_binary_matrix


Breast cancer samples and their respective mutations downloaded from the Cancer Cancer Genome Atlas (TCGA), used in <cite>Gobbi et al.</cite>.
Germline mutations were filtered out of the list of reported mutations; synonymous mutations and mutations identified as benign and tolerated were also removed from the dataset. The bipartite graph resulting when considering this matrix as an incidence matrix has $n_r=757, n_c=9757, e=19758$  for an edge density equal to $0.27\%$.<p></p><p></p>

datasets

Fast functions for bipartite network rewiring through N consecutive switching steps (See References) and for the computation of the minimal number of switching steps to be performed in order to maximise the dissimilarity with respect to the original network. Includes functions for the analysis of the introduced randomness across the switching steps and several other routines to analyse the resulting networks and their natural projections. Extension to undirected networks and directed signed networks is also provided. Starting from version 1.9.7 a more precise bound (especially for small network) has been implemented. Starting from version 2.2.0 the analysis routine is more complete and a visual montioring of the underlying Markov Chain has been implemented.

Andrea Gobbi

BiRewire

High-performing routines for the randomization of a bipartite graph (or a binary event matrix), undirected and directed signed graph preserving degree distribution (or marginal totals)

BRCA_binary_matrix function

Source

Breast cancer samples and their respective mutations downloaded from the Cancer Cancer Genome Atlas (TCGA), used in <cite>Gobbi et al.</cite>.
Germline mutations were filtered out of the list of reported mutations; synonymous mutations and mutations identified as benign and tolerated were also removed from the dataset. The bipartite graph resulting when considering this matrix as an incidence matrix has $n_r=757, n_c=9757, e=19758$  for an edge density equal to $0.27%$.

BRCA_binary_matrix: TCGA Brest Cancer data

Description

Usage

Arguments

Source

References