Package 'trio' Title Testing of Snps and Snp Interactions in Case-parent Trio Studies
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چکیده
Description Testing SNPs and SNP interactions with a genotypic TDT. This package furthermore contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio logic regression, for imputing missing genotypes in trios, for simulating case-parent trios with disease risk dependent on SNP interaction, and for power and sample size calculation in trio data.
منابع مشابه
Package ‘ trio ’
Description Testing SNPs and SNP interactions with a genotypic TDT. This package furthermore contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio logic regression, for imputing missing genotypes in trios, for simulating case-parent tr...
متن کاملPackage 'triogxe' Title a Data Smoothing Approach to Explore and Test Gene-environment Interaction in Case-parent Trio Data
Description The package contains functions that 1) estimates gene-environment interaction between a SNP and a continuous non-genetic attribute by fitting a generalized additive model to case-parent trio data, 2) produces graphical displays of estimated interaction, 3) performs permutation test of gene-environment interaction; 4) simulates informative case-parent trios.
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Orofacial clefts, including cleft lip with or without palate (CL/P) and cleft palate (CP), are one of the most common congenital malformations in Asian populations, where the rate of incidence is higher than in European or other racial groups. A number of candidate genes have been identified for orofacial clefts, although no single candidate has been consistently identified in all studies. We p...
متن کاملCombining case-control and case-trio data from the same population in genetic association analyses: overview of approaches and illustration with a candidate gene study.
In genetic association studies, investigators compare allele or genotype frequencies in unrelated case and control subjects or examine preferential allele transmissions from parents to affected offspring. In many genetic case-control studies, the collection of DNA material extends to relatives such as parents of cases. Thus, case-control and case-parent trio association analyses are possible. W...
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Methods A GWAS using Gene Chip Human Mapping 250K Nsp arrays was performed in 35 trio sets. The patients were grouped into those having oligoarticular or polyarticular JIA and those having SoJIA. Case-control and trio analysis are performed with plink toolset to determine JIA associated SNPs in both patient groups and associated SNPs are prioritized according to their statistical and biological...
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