CnaGen

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")
    library("CnaGen")

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.

Documentation

Introduction to CnaGen	PDF
Quick examples	TXT

Details

License	Artistic-2.0
Version	2.1

Package Downloads

Package source (all OSs)

CnaGen_2.1.tar.gz

Links

Genome Alteration Print (GAP)	http://bioinfo-out.curie.fr/projects/snp_gap/
GPHMM	http://genecube.med.yale.edu:8080/GPHMM/
OncoSNP	https://sites.google.com/site/oncosnp/
MixHMM	http://genecube.med.yale.edu:8080/MixHMM/
GenoCNA	http://www.bios.unc.edu/~wsun/software/genoCN.htm
ASCAT	http://heim.ifi.uio.no/bioinf/Projects/ASCAT/