CNVineta: a data mining tool for large case-control copy number variation data sets.


CNVineta is a flexible data mining tool for the analysis of copy number variations (CNVs) in large case-control SNP array data sets. The tool is available as an R statistical package. CNVineta offers a flexible and fast access to CNVs by a quick graphical overview in large case-control datasets. In addition, CNVineta provides rapid access to the log2 of raw data ratios (LRR) and B-allele frequencies (BAF) of specific or all samples, thereby allowing for a fast verification of the underlying raw data. CNVineta is also equipped with analysis methods for genome-wide screening for associated rare as well as common CNVs. Hence, CNVineta is a unique data mining tool to rapidly explore CNVs in large case-control data sets.


The CNVineta R package

CNVineta_1.0-1.tar.gz for Linux/Unix ... for Windows

Convert CNV calls to CNVineta format

Illumina to CNVineta java application Illumina to CNVineta full example
Affymetrix Power Tools to CNVineta full example QuantiSNP to CNVineta full example

CNVineta HapMap Data Download

Affymetrix Genome-Wide Human SNP Array 6.0 data set analyzed with Affymetrix Power Tools and converted to CNVineta format. Downloadable as splitted zip or splitted tar.gz archive. Each archive file set is about 2.7 GB. Download either the complete zip or tar.gz fileset (4 files), and unpack at your computer. 

Download md5sum 1a0e86ead50fcf0f1477a51c2520f34d
CNVineta.HapMap.Affy6.0.APT.dataset.z01 a29f000c097c46b2b06e797587989007
CNVineta.HapMap.Affy6.0.APT.dataset.z02 e92e3130543a37d7083a2209cc8527ce
CNVineta.HapMap.Affy6.0.APT.dataset.z03 c542b95b670e7d85501dd637d4b32af1


Download md5sum
CNVineta.HapMap.Affy6.0.APT.dataset.tar.gz.00 9b89912de09387ac06e205692cb9fe08
CNVineta.HapMap.Affy6.0.APT.dataset.tar.gz.01 61f766d131ce041c89d0ecf3765e194c
CNVineta.HapMap.Affy6.0.APT.dataset.tar.gz.02 ed211d0a5cdc6cd505211be74edc8d28
CNVineta.HapMap.Affy6.0.APT.dataset.tar.gz.03 6df124590d86adeff12309d9e3f58482

Change Log


  • stats of visualizeRegion: counts CNVs and calculates p-values for the segments which overlap the requested area only. Not for the entire picture/plot
  • visualizeRegion(): additional graphical parameters. plot.pch for point type. for point size. fixed.LRR.scale= FALSE/TRUE for the same y-axis scale for all LRR plots of the same region


  • dox0(): visualizes all CNVs within the visualized region and does not skip CNVs any more which do not overlap the area/"atom" of interest.
  • dox0(): can run multiple rules in one step. E.g. min.diff=c(3,5) and,1) allowing for the 3/0 and 5/1 screening in a single run


  • dox0(): running chromosome wise now => less memory required
  • a few changes regarding exception handling of different functions


  • removeChromosomeData(): "empty query" bug fixed, LRR plot for Illumina data bug fix (rs prefix for Illumina SNP marker)


  • QQ plots, Manhattan plots, Bonferroni's correction for multiple testing, CNV load and LRR based glm implemented.
  • minor changes regarding exception handling on missing or wrong input
  • major changes in the user guide (v1.8 to v1.9)


  • Help page for do.log.regression more detailed
  • "get Raw data failed" error message now explains for which subset it failed, when called from getHeatmap
  • minor changes in the user guide (v1.7 to v1.8)


This is the online resource for CNVineta. Recent package versions, tutorial updates and example data sets are available here. If you have any questions, please post at our CNVineta google group.


May 23 2011: CNVineta_1.0-1 released

Dec. 16 2010: CNVineta_1.0 released

Sep. 03 2010: CNVineta_0.9-9 released

July 01 2010: minor updates CNVineta_0.9-8

June 30 2010: manuscript accepted for publication, PMID: 20605930

June 05 2010: publication resubmitted to Bioinformatics

June 01 2010: new website section for data conversion

May 28 2010: major updates CNVineta_0.9-7

Feb. 10 2010: minor updates CNVineta_0.9-6

Feb. 02 2010: publication submitted to Bioinformatics


Institute of Clinical Molecular Biology

Christian-Albrechts-University zu Kiel

Schittenhelmstr. 12

D-24105 Kiel