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.
|Illumina to CNVineta java application||Illumina to CNVineta full example|
|Affymetrix Power Tools to CNVineta full example||QuantiSNP to CNVineta full example|
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.
- 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. plot.dot.cex 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 max.one.side=c(0,1) 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