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

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 <Emphasis Type="Bold">minPtest R package provides the first widely accessible implementation of a gene region-level summary for each candidate gene using the min <InlineEquation ID="IEq1"> <EquationSource Format="TEX">$$P$$</EquationSource> </InlineEquation> 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 <Emphasis Type="Bold">R packages, and automatically selects the most appropriate one for the study design at hand. The implementation of the <Emphasis Type="Bold">minPtest integrates two different parallel computing packages, thus optimally leveraging available resources for speedy results. Copyright Springer-Verlag Berlin Heidelberg 2014