minPtest: a resampling based gene region-level testing procedure for genetic case-control studies

Stefanie Hieke (), Harald Binder, Alexandra Nieters and Martin Schumacher

Computational Statistics, 2014, vol. 29, issue 1, 63 pages

Abstract: Current technologies generate a huge number of single nucleotide polymorphism (SNP) genotype measurements in case-control studies. The resulting multiple testing problem can be ameliorated by considering candidate gene regions. The minPtest R package provides the first widely accessible implementation of a gene region-level summary for each candidate gene using the min $$P$$ test. The latter is a permutation-based method that can be based on different univariate tests per SNP. The package brings together three different kinds of tests which were scattered over several R packages, and automatically selects the most appropriate one for the study design at hand. The implementation of the minPtest integrates two different parallel computing packages, thus optimally leveraging available resources for speedy results. Copyright Springer-Verlag Berlin Heidelberg 2014

Keywords: Single nucleotide polymorphism; Gene region-level summary; min $$P$$ test; Permutation-based resampling (search for similar items in EconPapers)
Date: 2014
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DOI: 10.1007/s00180-012-0391-4

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