Supplementary information for the paper:

Stationary Wavelet Denoising for Unequally Spaced Array-Based DNA Copy Number Data

Yuhang Wang, Siling Wang

1. Software with both graphical and command-line user interfaces for MS Windows is freely available for academic users. You can download it here. For usage, please check out the installation guide and the user manual.

2. Matlab code and data for generating the synthetic data used in the paper: gen_syntheticDCN.m, load_distri.m, dist_distr.txt, nonzero_length_distr.txt, zero_length_distr.txt.
Example usage:

>> load_distri;
>> gen_syntheticDCN(1000, 200000, 0.2, nonzero_length_distr,zero_length_distr,dist_distr);

This will generate synthetric DNA copy number data (log2 rations) on 1000 artificial chromosomes with length 200000 kb. The standard deviation for gaussian noise is 0.2. nonzero_length_distr is the empirical distribution of lengths of chromosomal regions with DCN != 2; zero_length_distr is the empirical distribution of lengths of chromosomal regions with DCN == 2; dist_distr is the empirical distribution of distances bewteen probes.

3. Processed GBM array CGH data used in the paper:
GBM29Chr7.dcn, GBM29Chr7_chrlen.ini
GBM31Chr13.dcn, GBM31Chr13_chrlen.ini

All normalized GBM data can be found here.