BRCA_binary_matrix: TCGA Brest Cancer data

In 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)

Description

Breast cancer samples and their respective mutations downloaded from the Cancer Cancer Genome Atlas (TCGA), used in Gobbi et al.. 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\%.

Usage

data(BRCA_binary_matrix)

Source

http://tcga.cancer.gov/dataportal/

References

Gobbi, A. and Iorio, F. and Dawson, K. J. and Wedge, D. C. and Tamborero, D. and Alexandrov, L. B. and Lopez-Bigas, N. and Garnett, M. J. and Jurman, G. and Saez-Rodriguez, J. (2014) Fast randomization of large genomic datasets while preserving alteration counts Bioinformatics 2014 30 (17): i617-i623 doi: 10.1093/bioinformatics/btu474.

BiRewire documentation built on Nov. 8, 2020, 8:09 p.m.