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Bioinformatics. 2011 Feb 1;27(3):419-20. doi: 10.1093/bioinformatics/btq668. Epub 2010 Dec 5.

Rseg--an R package to optimize segmentation of SNP array data.

Author information

1
Department of Molecular Medicine, Aarhus University Hospital Skejby, Aarhus N, Denmark. plamy@cs.au.dk

Abstract

The use of high-density SNP arrays for investigating copy number alterations in clinical tumor samples, with intra tumor heterogeneity and varying degrees of normal cell contamination, imposes several problems for commonly used segmentation algorithms. This calls for flexibility when setting thresholds for calling gains and losses. In addition, sample normalization can induce artifacts in the copy-number ratios for the non-changed genomic elements in the tumor samples.

RESULTS:

We present an open source R package, Rseg, which allows the user to define sample-specific thresholds to call gains and losses. It also allows the user to correct for normalization artifacts.

AVAILABILITY:

The R package, Rseg, is available at: http://www.cs.au.dk/~plamy/Rseg/ and runs on Linux and MS-Windows.

PMID:
21134892
DOI:
10.1093/bioinformatics/btq668
[Indexed for MEDLINE]
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