for Download

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

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

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.