Generation of synthetic data to emulate tumour samples on SNP arrays

CnaGen version: Release (2.1)

Generation of synthetic SNP-array tumour samples with extensive parameterization. Normal cell contamination, intra-tumour heterogeneity, genomic waves, baseline shift and other known factors are parameterizable.

Author, mantainer: D. Mosén-Ansorena

To install this package, regardless of the operating system, enter:

    install.packages("CnaGen_2.1.tar.gz", repos=NULL, type="source")

Change log

Version 2.1

  • Important fix: fixed BAF calculation on regions with intra-tumour heterogeneity.
  • Bug fix: SNP heterozygosity option was always based on first SNP.
  • Added: new options distSNP and varDistSNP control distances between SNPs.

Version 2.0.1

  • Critical fix: please update to this version for critical fix.

Version 2.0

  • Bug fix: PFB sampling optimization.
  • Changed: LRR baseline shift is now automatically estimated by default.
  • Added: New hybrid mode: ability to define a copy number scaffold pattern.

Version 1.1.2

  • Bug fix: annotation change to reflect that simple copy number 1 alterations are always LOH events.

Version 1.1

  • Bug fix: subclones of complex CNAs can now randomly have any allelic ratio.
  • Changed: LRR and BAF noise levels are now measured in standard deviations.
  • Added: R data files of samples now contain information on their DNA index and LRR shift.
  • Added: LRR shift can be automatically estimated from the DNA index through an empirical formula.

Version 1.0

  • Initial release.


Introduction to CnaGen PDF
Quick examples TXT


License Artistic-2.0
Version 2.1

Package Downloads

Package source (all OSs) CnaGen_2.1.tar.gz


Genome Alteration Print (GAP)

Examples »

In this file you will find some quick examples. For a full introduction to the package, please refer to the 'Introduction to CnaGen' PDF document.

Quick examples  

Contact »

You can contact me for any questions, found bugs and suggestions at the following direction: _at_ cicbiogune _dot_ es

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