Dataset Information

Isqg: A Binary Framework for in Silico Quantitative Genetics.

ABSTRACT: The dna is the fundamental basis of genetic information, just as bits are for computers. Whenever computers are used to represent genetic data, the computational encoding must be efficient to allow the representation of processes driving the inheritance and variability. This is especially important across simulations in view of the increasing complexity and dimensions brought by genomics. This paper introduces a new binary representation of genetic information. Algorithms as bitwise operations that mimic the inheritance of a wide range of polymorphisms are also presented. Different kinds and mixtures of polymorphisms are discussed and exemplified. Proposed algorithms and data structures were implemented in C++ programming language and is available to end users in the R package "isqg" which is available at the R repository (cran). Supplementary data are available online.

SUBMITTER: Toledo FH

PROVIDER: S-EPMC6686941 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature

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isqg: A Binary Framework for <i>in Silico</i> Quantitative Genetics.

Toledo Fernando H FH Pérez-Rodríguez Paulino P Crossa José J Burgueño Juan J

G3 (Bethesda, Md.) 20190808 8

The dna is the fundamental basis of genetic information, just as bits are for computers. Whenever computers are used to represent genetic data, the computational encoding must be efficient to allow the representation of processes driving the inheritance and variability. This is especially important across simulations in view of the increasing complexity and dimensions brought by genomics. This paper introduces a new binary representation of genetic information. Algorithms as bitwise operations t ...[more]

PMID: 31201204

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Project description:Intersectionality recognizes that in the context of sociohistorically shaped structural power relations, an individual's multiple social positions or identities (e.g., gender, ethnicity) can interact to affect health-related outcomes. Despite limited methodological guidance, intersectionality frameworks have increasingly been incorporated into epidemiological studies, both to describe health disparities and to examine their causes. This study aimed to advance methods in intersectional estimation of binary outcomes in descriptive health disparities research through evaluation of 7 potentially intersectional data analysis methods: cross-classification, regression with interactions, multilevel analysis of individual heterogeneity (MAIHDA), and decision trees (CART, CTree, CHAID, random forest). Accuracy of estimated intersection-specific outcome prevalence was evaluated across 192 intersections using simulated data scenarios. For comparison we included a non-intersectional main effects regression. We additionally assessed variable selection performance amongst decision trees. Example analyses using National Health and Nutrition Examination Study data illustrated differences in results between methods. At larger sample sizes, all methods except for CART performed better than non-intersectional main effects regression. In smaller samples, MAIHDA was the most accurate method but showed no advantage over main effects regression, while random forest, cross-classification, and saturated regression were the least accurate, and CTree and CHAID performed moderately well. CART performed poorly for estimation and variable selection. Sensitivity analyses examining the bias-variance tradeoff suggest MAIHDA as the preferred unbiased method for accurate estimation of high-dimensional intersections at smaller sample sizes. Larger sample sizes are more imperative for other methods. Results support the adoption of an intersectional approach to descriptive epidemiology.

Dataset Information

Isqg: A Binary Framework for in Silico Quantitative Genetics.

Publications

isqg: A Binary Framework for <i>in Silico</i> Quantitative Genetics.

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