About | Publications | Software

reverseMA

An R package that examines mediation analysis in the presence of reverse causality. On GitHub and implements the method from the following paper:

• Lutz SM, Sordillo J, Hokanson JE, Wu AC, Lange C. (2020) The Effects of Misspecification of the Mediator and Outcome in Mediation Analysis. Gen Epi. (In Press).

RNAseqRare

An R package that examines expression quantitative trait loci (eQTL) analyses of rare variants for RNA-seq data. On GitHub and implements the method from the following paper:

• Lutz SM, Thwing A, Fingerlin TE. (2019) eQTL Mapping of Rare Variant Associations Using RNA-seq Data: An Evaluation of Approaches. PLoS ONE. (In Press).

ePowerLI

An R package that performs an empirical power analysis of the interaction of two normally distributed traits in longitudinal unbalanced datasets. On GitHub and implements the power analysis used in the following paper:

• Kelly RS, Sordillo JE, Lutz SM, Avila L, Soto-Quiros M, Celedón JC, McGeachie MJ, Dahlin A, Tantisira K, Huang M, Clish CB, Weiss ST, Lasky-Su J, Wu AC. (2019) Pharmacometabolomics of Bronchodilator Response in Asthma and the Role of Age-Metabolite Interactions. Metabolomics. (In Press)

gxeRC

An R package that examines SNP by environment interactions for both common and rare variants. On GitHub and implements the power analysis used in the following paper:

• Lutz SM, Frederiksen B, Begum F, Cho MH, Hobbs B, McDonald ML, Parker MM, DeMeo DL, Jiang L, Eringher M, Young K, Foreman MG, Kinney GL, Make BJ, Lomas DA, Bakke P, Gulsvik A, Crapo JD, Silverman EK, Beaty TH, Hokanson JE. (2018) Common and Rare Variants Genetic Association Analysis of Cigarettes Per Day Among Ever Smokers in COPD Cases and Controls. NTR. (In Press)

Umediation

An R package that examines the role of unmeasured confounding of the exposure-mediator-outcome relationship in mediation analysis. On GitHub and implements the method from the following paper:

• Lutz SM, Thwing A, Schmiege S, Kroehl M, Baker C, Starling A, Hokanon JE, Ghosh D. (2017) Examining the Role of Unmeasured Confounding in Mediation Analysis with Genetic and Genomic Applications. BMC Bioinformatics. 18(1):344.

pleiotropy

An R package that tests for common and rare variant associations with multiple phenotypes using the Hausdorff metric in a permutation based framework. On GitHub and implements the method from the following paper:

• Lutz SM, Fingerlin T, Hokanson JE, Lange C. (2016) A General Approach to Testing for Pleiotropy with Rare and Common Variants. Genetic Epidemiology. 41(2):163-170.

SecondaryPhenotype

An R package that adjusts for ascertainment bias when testing for genetic associations of secondary phenotypes in population based studies. On GitHub and implements the method from the following paper:

• Lutz SM, Hokanson JE, Lange C. (2014) An Alternative Hypothesis Testing Strategy for Secondary Phenotype Data in Case-Control Genetic Association Studies. Frontiers in Genetics. 5 (188).

NPBAT

An interactive software package for the analysis of population based genetic association studies. On Google Sites and implements the method from the following paper:

• Lutz SM, Yip WK, Hokanson JE, Laird N, Lange C. (2013) A General Semi-Parametric Approach to the Analysis of Genetic Association Studies in Population-Based Designs. BMC Genetics. 14(13).

CausalScreen

An R package that implements a screening step to increase power when testing for direct genetic effects of multiple SNPs in family based association studies using causal inference methodology. On GitHub and implements the methods from the following papers:

• Lutz SM, Vansteelandt S, Lange C. (2013) Testing for Direct Genetic Effects Using a Screening Step in Family-Based Association Studies. Frontiers in Genetics. 4 (243).

• Vansteelandt S, Goetgeluk S, Lutz S, Waldamn I, Lyon H, Schadt EE, Weiss ST, Lange C. (2009) On the Adjustment for Covariates in Genetic Association Analysis: A Novel, Simple Principle to Infer Direct Effects. Genetic Epidemiology. 33(5): 394-405.

bayesIndirect

An R package that examines the indirect effect of a SNP on the outcome through the mediator in a Bayesian framework with a spike and slab prior. On GitHub and implements the method from the following paper:

• Lutz SM, Hokanson JE, Sharma S, Weiss S, Raby B, Lange C. (2013) On the Integration of Expression Profiles in Genetic Association Studies: A Bayesian Approach to Determine the Path from Gene to Disease. Open Journal of Genetics. 3(3).

snpDRAC

An R package that examines power to detect a genetic association for dominant, recessive, additive, and co-dominant models. This R package was built as a learning tool for BST 227: Introduction to Statistical Genetics on GitHub.