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


BACKGROUND
The R package, Rseg, is available at: http://www.cs.au.dk/~plamy/Rseg/ and runs on Linux and MS-Windows.
Department of Molecular Medicine, Aarhus University Hospital Skejby, Aarhus N, Denmark. plamy@cs.au.dk
Philippe
P
Lamy
Carsten
C
Wiuf
Torben F
TF
Ørntoft
Claus L
CL
Andersen
D000465:Algorithms; D023281:Genomics / Q000379:methods*; D006801:Humans; D009369:Neoplasms / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D012984:Software