MxE.power: Power Calculations for DNA Methylation Association Tests Leveraging Methylome-Environment Interaction
- Download R function here, courtesy of Emily Slade (April 2016)
- Reference: Slade, E. & Kraft, P. (2016). Leveraging methylome-environment interaction to detect genetic determinants of disease. Hum Hered, 8(1): 26-34.
GEmis: Power Calculations for Gene-Environment Tests Incorporating Misclassified Exposures
- SAS Macro (courtesy of Sara Lindstrom). [3 March 2009]
- Complete table of power calculations summarized in Lindstrom et al. (2009).
- Reference: Lindstrom S, Spiegelman D, Kraft P. Hum Hered. 2009;68(3):171-181.
PowerGxE: Power Calculations for Genetic Association Tests Exploiting Gene-environment Interaction
- SAS Macro (courtesy of Yu-Chun Jean Yen).
- Reference: Kraft P, Yen YC et al. Hum Hered (2007) 63:111-119.
GECOR: Power for Gene-Environment Interaction Tests in Matched Case-Control Association Studies, Allowing for Correlated Environmental Exposures
- R functions, GUI front end, examples and manual (courtesy of Amy Murphy).
- Reference: Murphy and Kraft, submitted to Genetic Epidemiology.
MULTIPOW 2.1: Power for Multi-stage Genome-wide Association Studies
- R functions, examples and manual.
- Old version (replication-based power only).
- These functions are useful for designs with more than two stages. For two stages, I recommend the much more user-friendly CATS or the method described in Wang et al. (2006) Genet Epidemiol 30:356.
Macros for the Breast and Prostate Cancer Cohort Consortium
- Analysis utilities and formats [Last modified 8 June 2006].
- Code to generate allele and genotype frequencies, departures from HWE etc. [Last modified 17 March 2006].
- Haplotype imputation macro (PC) [Last modified 8 June 2006].
- Zipped documentation and sample code from 15 Oct 2005 workshop.
HAPPY: Haplotype Scoring for Generalized Linear Modeling and Haplotype-Disease Association Tests
- IMPORTANT NOTE: due to changes in PROC HAPLOTYPE syntax “caco” option is unsupported in %happy for Version 9
- SAS macro [Last modified 19 Mar 2006], manual, and sample code and data.
- Older version of SAS macro [Last modified Jul 2004] that is compatible with old-style (pre-version 9.1) PROC HAPLOTYPE syntax.
- Reference: Kraft P et al. (2005) Genet Epidemiol 28:261-72.
WANDEL: Permutation adjustment for multiple testing
MOFET: Maternal-Fetal Genotype Interaction Tests
- SAS macro [Last modified 29 July 2004] and corresponding manual.
- References: Kraft P et al. Euro J Hum Genet (2004) 12:192-8; Kraft P et al. Genet Epidemiol (2005) 29:87-90.
MISOR: Odds ratios for phase-known haplotypes measured with error
- R function and example code [Last modified 13 March 2006].
- Reference: Govindarajulu et al. (submitted).
FEXAT: Family-based Expression-Association Test
[Last modified March 2003].
- Gzipped Linux executable (courtesy of Jason Aten) [Last modified March 2003]. Help file.
- Reference: Kraft P et al. (2003) Am J Hum Genet 72:1323-30.