p_ACT

p_ACT is an R program that adjusts sets of up to 500 p-values from association tests between correlated traits and SNPs for multiple testing, accounting for the correlation between tests.

Version 1.0 of P_ACT was the initial release to the public.

Version 1.1 is modified to allow omission of the traits.txt file when only one trait is considered, and omission of the genotype.txt file and the covar.txt file when only one genotype is considered.

Version 1.2 contains two fixes for p_ACT_seq.R (no changes were made to p_ACT.R in this version). The first prevents p_ACT_seq.R from crashing when all tests are significant. The second ensures the proper ordering of tests in the covariance matrix regardless of how the traits and SNPs are ordered in the input files.

The file p_ACT distribution includes the following:

• README.txt: a description of how to run p_ACT.R and proper input file formats
• p_ACT.R: R program for non-sequential p_ACT; adjusts only the minimum p-value of a set.
• p_ACT_seq.R: R program for sequential p_ACT; adjusts all p-values for which p_ACT < alpha.
• Sample Files: A directory containing sample input and output files

Please use this citation in your publications:

Conneely, K.N. and Boehnke, M. (2007) So many correlated tests, so little time! Rapid adjustment of p-values for multiple correlated tests. American Journal of Human Genetics 81:1158-1168.

Please take the time to register so we might notify you of future changes. Thank you!

Download Program Directly

p_ACT_1.2.tar.gz