Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Fast and Robust Segmentation of Copy Number Profiles Using Multi-Scale Edge Detection

Ivo W Kwee, Andrea Rinaldi, Cassio Polpo de Campos, Francesco Bertoni
doi: https://doi.org/10.1101/056705
Ivo W Kwee
1Lymphoma and Genomics Research Program, Institute of Oncology Research, Bellinzona, Switzerland.
2Dalle Molle Institute for Artificial Intelligence, Manno, Switzerland.
3Swiss Institute of Bioinformatics, Lausanne, Switzerland.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Andrea Rinaldi
1Lymphoma and Genomics Research Program, Institute of Oncology Research, Bellinzona, Switzerland.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Cassio Polpo de Campos
2Dalle Molle Institute for Artificial Intelligence, Manno, Switzerland.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Francesco Bertoni
1Lymphoma and Genomics Research Program, Institute of Oncology Research, Bellinzona, Switzerland.
4Lymphoma Unit, IOSI, EOC, Bellinzona, Switzerland.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

ABSTRACT

Raw copy number data is highly dimensional, noisy and can suffer from so-called genomic wave artifacts. We introduce a novel method based on multi-scale edge detection in derivative space. By using derivatives, the algorithm was very fast and robust against genomic waves. Our method compared very well to existing state-of-the-art segmentation methods and importantly outperformed these if noise and wave artifacts were well present.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted June 02, 2016.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Fast and Robust Segmentation of Copy Number Profiles Using Multi-Scale Edge Detection
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Fast and Robust Segmentation of Copy Number Profiles Using Multi-Scale Edge Detection
Ivo W Kwee, Andrea Rinaldi, Cassio Polpo de Campos, Francesco Bertoni
bioRxiv 056705; doi: https://doi.org/10.1101/056705
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Fast and Robust Segmentation of Copy Number Profiles Using Multi-Scale Edge Detection
Ivo W Kwee, Andrea Rinaldi, Cassio Polpo de Campos, Francesco Bertoni
bioRxiv 056705; doi: https://doi.org/10.1101/056705

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3477)
  • Biochemistry (7315)
  • Bioengineering (5290)
  • Bioinformatics (20180)
  • Biophysics (9967)
  • Cancer Biology (7696)
  • Cell Biology (11242)
  • Clinical Trials (138)
  • Developmental Biology (6413)
  • Ecology (9910)
  • Epidemiology (2065)
  • Evolutionary Biology (13266)
  • Genetics (9346)
  • Genomics (12542)
  • Immunology (7665)
  • Microbiology (18919)
  • Molecular Biology (7413)
  • Neuroscience (40853)
  • Paleontology (298)
  • Pathology (1224)
  • Pharmacology and Toxicology (2124)
  • Physiology (3137)
  • Plant Biology (6833)
  • Scientific Communication and Education (1268)
  • Synthetic Biology (1890)
  • Systems Biology (5295)
  • Zoology (1083)