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BMCBI
2010

R-Gada: a fast and flexible pipeline for copy number analysis in association studies

8 years 7 months ago
R-Gada: a fast and flexible pipeline for copy number analysis in association studies
Background: Genome-wide association studies (GWAS) using Copy Number Variation (CNV) are becoming a central focus of genetic research. CNVs have successfully provided target genome regions for some disease conditions where simple genetic variation (i.e., SNPs) has previously failed to provide a clear association. Results: Here we present a new R package, that integrates: (i) data import from most common formats of Affymetrix, Illumina and aCGH arrays; (ii) a fast and accurate segmentation algorithm to call CNVs based on Genome Alteration Detection Analysis (GADA); and (iii) functions for displaying and exporting the Copy Number calls, identification of recurrent CNVs, multivariate analysis of population structure, and tools for performing association studies. Using a large dataset containing 270 HapMap individuals (Affymetrix Human SNP Array 6.0 Sample Dataset) we demonstrate a flexible pipeline implemented with the package. It requires less than one minute per sample (3 million probe...
Roger Pique-Regi, Alejandro Cáceres, Juan R
Added 09 Dec 2010
Updated 09 Dec 2010
Type Journal
Year 2010
Where BMCBI
Authors Roger Pique-Regi, Alejandro Cáceres, Juan R. González
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