TitanCNA-dataset: TITAN EM trained results for an example dataset

In TitanCNA: Subclonal copy number and LOH prediction from whole genome sequencing of tumours

Description

Data for chromosome 2 for a triple-negative breast cancer dataset and the expectation-maximization (EM) trained results. Only 20,000 datapoints are included and the data has been scrambled to anonymize patient SNPs.

data

Processed input data that is first generated by loadAlleleCounts, and includes log ratios that have been GC content and mappability corrected using correctReadDepth

.

convergeParams

EM results that are generated by runEMclonalCN

Usage

  data(EMresults)

Format

‘data’ is a list. ‘convergeParams’ is a list.

References

Shah SP et al. (2012). The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature, 486(7403): 395-399. (PMID: 22495314)

Ha, G., Roth, A., Lai, D., Bashashati, A., Ding, J., Goya, R., Giuliany, R., Rosner, J., Oloumi, A., Shumansky, K., Chin, S.F., Turashvili, G., Hirst, M., Caldas, C., Marra, M. A., Aparicio, S., and Shah, S. P. (2012). Integrative analysis of genome wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple negative breast cancer. Genome Research, 22(10):1995,2007. (PMID: 22637570)

Ha, G., Roth, A., Khattra, J., Ho, J., Yap, D., Prentice, L. M., Melnyk, N., McPherson, A., Bashashati, A., Laks, E., Biele, J., Ding, J., Le, A., Rosner, J., Shumansky, K., Marra, M. A., Huntsman, D. G., McAlpine, J. N., Aparicio, S. A. J. R., and Shah, S. P. (2014). TITAN: Inference of copy number architectures in clonal cell populations from tumour whole genome sequence data. Genome Research, 24: 1881-1893. (PMID: 25060187)

TitanCNA documentation built on Nov. 8, 2020, 8:14 p.m.