Summary: 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.