Software

Software

GEmis: Power Calculations for Gene-Environment Tests Incorporating Misclassified Exposures

SAS Macro (courtesy of Sara Lindstrom). [New (3 March 2009)!]

Complete table of power calculations summarized in Lindstrom et al. (2009).

Reference: Lindstrom S, Spiegelman D, Kraft P Hum Hered (in press).

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

SAS macro, and example code, log, and output [Last modified 28 Feb 2006].

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

R function

[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.

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Last updated: 20 March 2007.