Polyunphased: an extension to polytomous outcomes of the Unphased package for family-based genetic association analysis
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Alexandre Bureau
und
Jordie Croteau
Abstract
Polytomous phenotypes arise when a disease has multiple subtypes or when two dichotomous phenotypes are analyzed simultaneously. Few software programs offer the option to analyze such phenotypes in family studies, and none implements conditional polytomous logistic regression for within-family analysis robust to population stratification. We introduce Polyunphased, an extension to polytomous phenotypes of the Unphased package, a flexible software tool for genetic association analysis in nuclear families. Like Unphased, Polyunphased is written in C++ and runs from the command line or from a Java graphical user interface. Most Unphased options remain available in Polyunphased, including those handling missing parental genotypes while preserving robustness to population stratification, and the modelling options. Simulation studies confirmed the expected statistical behaviour of the maximum likelihood estimates of the association parameters of the conditional logistic regression model when the corresponding association parameters in the parental term of the likelihood function are set to 0, but revealed convergence problems when estimating these parental association parameters separately. The former approach is thus recommended with polytomous phenotypes.
References
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©2017 Walter de Gruyter GmbH, Berlin/Boston
Artikel in diesem Heft
- Frontmatter
- Research Articles
- Statistical models and computational algorithms for discovering relationships in microbiome data
- Binary Markov Random Fields and interpretable mass spectra discrimination
- Comparison and visualisation of agreement for paired lists of rankings
- Bivariate Poisson models with varying offsets: an application to the paired mitochondrial DNA dataset
- Generalized partial linear varying multi-index coefficient model for gene-environment interactions
- Software and Application Note
- Polyunphased: an extension to polytomous outcomes of the Unphased package for family-based genetic association analysis
Artikel in diesem Heft
- Frontmatter
- Research Articles
- Statistical models and computational algorithms for discovering relationships in microbiome data
- Binary Markov Random Fields and interpretable mass spectra discrimination
- Comparison and visualisation of agreement for paired lists of rankings
- Bivariate Poisson models with varying offsets: an application to the paired mitochondrial DNA dataset
- Generalized partial linear varying multi-index coefficient model for gene-environment interactions
- Software and Application Note
- Polyunphased: an extension to polytomous outcomes of the Unphased package for family-based genetic association analysis
