Visualization of genomic changes by segmented smoothing using an L0 penalty.
Copy number variations (CNV) and allelic imbalance in tumor tissue can show strong segmentation. Their graphical presentation can be enhanced by appropriate smoothing. Existing signal and scatterplot smoothers do not respect segmentation well. We present novel algorithms that use a penalty on the L(0) norm of differences of neighboring values. Visualization is our main goal, but we compare classification performance to that of VEGA.
Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands. R.C.A.Rippe@lumc.nl
Ralph C A
RC
Rippe
Jacqueline J
JJ
Meulman
Paul H C
PH
Eilers
D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D056915:DNA Copy Number Variations / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics; D006801:Humans