Copynumber: Efficient algorithms for single- and multi-track copy number segmentation.

ABSTRACT:

Background

Cancer progression is associated with genomic instability and an accumulation of gains and losses of DNA. The growing variety of tools for measuring genomic copy numbers, including various types of array-CGH, SNP arrays and high-throughput sequencing, calls for a coherent framework offering unified and consistent handling of single- and multi-track segmentation problems. In addition, there is a demand for highly computationally efficient segmentation algorithms, due to the emergence of very high density scans of copy number.

Results

A comprehensive Bioconductor package for copy number analysis is presented. The package offers a unified framework for single sample, multi-sample and multi-track segmentation and is based on statistically sound penalized least squares

SUBMITTER: Nilsen G 

PROVIDER: S-EPMC3582591 | biostudies-literature | 2012 Nov

REPOSITORIES: biostudies-literature