Motivation: Knowing the exact locations of multiple change points in genomic sequences serves several biological needs, for instance when data represent aCGH profiles and it is of interest to identify possibly damaged genes involved in cancer and other diseases. Only a few of the currently available methods deal explicitly with estimation of the number and location of change points, and moreover these methods may be somewhat vulnerable to deviations of model assumptions usually employed. Results: We present a computationally efficient method to obtain estimates of the number and location of the change points. The method is based on a simple transformation of data and it provides results quite robust to model misspecifications. The efficiency of the method guarantees moderate computational times regardless of the series length and the number of change points. Availability: The methods described in this article are implemented in the new R package cumSeg available from the Comprehensive R Archive Network at http://CRAN.R-project.org/package=cumSeg. Contact:vito.muggeo@unipa.it Supplementary information: Supplementary data are available at Bioinformatics online.

We introduce a score-type statistic to test for a non-zero regression coefficient when the relevant term involves a nuisance parameter present only under the alternative. Despite the non-regularity and complexity of the problem and unlike the previous approaches, the proposed test statistic does not require the nuisance to be estimated. It is simple to implement by relying on the conventional distributions, such as Normal or t, and it justified in the setting of probabilistic coherence. We focus on testing for the existence of a breakpoint in segmented regression, and illustrate the methodology with an analysis on data of DNA copy number aberrations and gene expression profiles from 97 breast cancer patients; moreover some simulations reveal that the proposed test is more powerful than its competitors previously discussed in literature.

We present a simple and effective iterative procedure to estimate segmented mixed models in a likelihood based framework. Random effects and covariates are allowed for each model parameter, including the changepoint. The method is practical and avoids the computational burdens related to estimation of nonlinear mixed effects models. A conventional linear mixed model with proper covariates that account for the changepoints is the key to our estimating algorithm. We illustrate the method via simulations and using data from a randomized clinical trial focused on change in depressive symptoms over time which characteristically show two separate phases of change.