SST: Subset multiple hypothesis testing procedure to combine two...

Description Usage Arguments Value References See Also

View source: R/sst.R


Run SST to adjust for multiple testing while combining two steps of the GxE interaction testing procedure. The procedure is applicable for a multivariate phenotype, as well as a univariate phenotype.


SST(PVAL, Pg_thr_step1 = 0.005, FWER_step2 = 0.05)



A data.frame with three columns. The first column (PVAL$SNP) provides the name of all SNPs or genetic variants tested. Second column (PVAL$G.P) contains the p-values of the variants obtained from testing an overall marginal genetic association between the multivariate phenotype and each genetic variant individually. And the third column (PVAL$GE.P) contains the p-values obtained from testing overall GxE effect on the multivariate phenotype in presence of possible marginal effect due to the genetic variant and a marginal effect due to the environmental variable. Number of rows in PVAL is the same as the number of genetic variants, and it has the same structure as in the output of mv_G_GE. No default.


A positive real number between 0 and 1 providing the p-value threshold to select the set of promising SNPs in step 1. These selected SNPs will be tested for GxE effect in the second step. Default is 0.005.


A positive real number between 0 and 1 specifying the family-wise error rate to be maintained in the second step while identifying the genetic variants having a genome-wide significant overall GxE effect on the multivariate phenotype. Default is 0.05.


The output is a vector of SNPs identified to have a genome-wide significant overall GxE effect.


A Majumdar, KS Burch, S Sankararaman, B Pasaniuc, WJ Gauderman, JS Witte (2020) A two-step approach to testing overall effect of gene-environment interaction for multiple phenotypes. bioRxiv, doi:

See Also

WHT, mv_G_GE

MPGE documentation built on Jan. 8, 2021, 2:28 a.m.