UNDERGRAD RESEARCH

Software

This page contains links to software that has resulted from our research.

Combining rare-variant tests of association

R version combotests.R tests.R

Reference: Greco B, Hainline A, Arbet J, Grinde K, Benitez A and Tintle NL (2015) "A general approach for combining diverse rare variant assocaition tests provides improved robustness across a wider range of genetic architecture" European journal of human genetics. To appear.

Testing for differences in metabotypes

R version software.Rotherfunctions.R, LRT.case.control.R, D9D_C16.csv

Reference: Tintle NL, Newman J, Shearer G (2015) "A novel approach to identify optimal metabotypes of elongase and desaturase activities in prevention of acute coronary syndrome" Metabolomics. To appear.

 

Impact of genotype errors on rare variant tests of association

R version Software

Reference: Cook K*, Benitez A*, Fu C*, Tintle NL (2014) "Evaluating the impact of genotype errors on rare variant tests of association" In revision.

 

Testing genotype-phenotype association with duplicate genotype data

General test of independence

R version Software and Instructions

SAS version Software and Instructions

Reference: Tintle NL, Gordon D, McMahon F, and Finch SJ (2007) "Using duplicate genotyped data in genetic analyses: Testing association and estimating error rates." Statistical applications in genetics and molecular biology. 6:4. Full text.

Linear trend test Estimation Software and Design Software

Reference: Borchers B, Brown M, McLellan B, Bekmetjev A, and Tintle NL (2009) "Incorporating duplicate genotype data into linear trend tests of genetic association: Methods and cost-effectiveness." Statistical Applications in Genetics and Molecular Biology. 8:24. Full text.

 

Cost-effectiveness of duplicate genotyping

General test of independence Design Software

Reference: Tintle NL, Gordon D, Van Bruggen D, and Finch SJ (2009) "The cost effectiveness of duplicate genotyping for testing genetic association." Annals of Human Genetics. 73, 370-378.

 

Cost-effectiveness of reclassification sampling

Estimation Software and Instructions

Reference: Bekmetjev A , VanBruggen D , McLellan B , DeWinkle B , Lunderberg E , et al. 2012 The Cost-Effectiveness of Reclassification Sampling for Prevalence Estimation. PLoS ONE 7(2): e32058. doi:10.1371/journal.pone.0032058

 

Single Nucleotide Variant (polymorphism) set testing software (SNVset)

R package (PRELIMINARY VERSION: 2012-07-06)

User guide

Reference: Peterson, A., Spratt, J., and Tintle, N. “Incorporating prior knowledge in GWAS” in Genome-Wide Association Studies, ed. Cedric Gondro, Julius van der Werf, and Ben Hayes. Humana Press. To appear.