Loading...
Please wait, while we are loading the content...
FocalCall: An R Package for the Annotation of Focal Copy Number Aberrations
| Content Provider | SAGE Publishing |
|---|---|
| Author | Krijgsman, Oscar Benner, Christian Meijer, Gerrit A. Mark A. van de Wiel Ylstra, Bauke |
| Copyright Year | 2014 |
| Abstract | In order to identify somatic focal copy number aberrations (CNAs) in cancer specimens and to distinguish them from germ-line copy number variations (CNVs), we developed the software package FocalCall. FocalCall enables user-defined size cutoffs to recognize focal aberrations and builds on established array comparative genomic hybridization segmentation and calling algorithms. To distinguish CNAs from CNVs, the algorithm uses matched patient normal signals as references or, if this is not available, a list with known CNVs in a population. Furthermore, FocalCall differentiates between homozygous and heterozygous deletions as well as between gains and amplifications and is applicable to high-resolution array and sequencing data.AVAILABILITY AND IMPLEMENTATION:FocalCall is available as an R-package from: https://github.com/OscarKrijgsman/focalCall. The R-package will be available in Bioconductor.org as of release 3.0. |
| Related Links | https://journals.sagepub.com/doi/pdf/10.4137/CIN.S19519?download=true |
| ISSN | 11769351 |
| Volume Number | 13 |
| Journal | Cancer Informatics (CIX) |
| e-ISSN | 11769351 |
| DOI | 10.4137/CIN.S19519 |
| Language | English |
| Publisher | Sage Publications UK |
| Publisher Date | 2014-12-01 |
| Publisher Place | London |
| Access Restriction | Open |
| Rights Holder | © 2014 SAGE Publications. |
| Subject Keyword | DNA copy number aCGH focal CNAs R-package sequencing |
| Content Type | Text |
| Resource Type | Article |
| Subject | Cancer Research Oncology |
