Nov 8, 2020 · minP test - minP test considered the significant of the observed minimum p-value. Significance is computed by integrating the multivariate normal distribution with covariance Σ as proposed in Conneelly and Boehnke (2008).

Permutation-based p-values estimation via min P test, a gene region-level summary for each candidate gene. The gene region-level summary assesses the smallest p-trend within each gene region comparing cases and controls.

minPtest <- function (y,x,SNPtoGene,formula=NULL,cov=NULL,matchset=NULL,permutation=1000, seed=NULL,subset=NULL,parallel=FALSE,ccparallel=FALSE,trace=FALSE, aggregation.fun=min,adj.method=c ("bonferroni","holm","hochberg","hommel","BH","BY","fdr","none"), ...) { call <- match.call () …

In other words, one could construct a valid minP test for G-E interaction with an ‘AE’ model instead of an ‘ACE’ model, where the random effect ‘A’ in the ‘AE’ model captures the effect of genetic and shared environmental effect in twins.

Oct 2, 2009 · Here we propose a general framework under logistic regression to contrast both genotype scores and LD patterns simultaneously. The basic idea is to incorporate some terms measuring LD patterns, in addition to genotype scores, …

These functions compute permutation adjusted p -values for the step-down maxT and minP multiple testing procedures, which provide strong control of the family-wise Type I error rate (FWER).

The minimum of the p-values (MinP) of multiple phenotypes has been proposed as a testing statistic (Conneely and Boehnke, 2007). The MinP method is powerful when a SNP affects only a very small number of multiple phenotypes, but is less powerful in the presence of denser signals.

May 2, 2019 · If users want to compare LGRF with the minimum p-value (MinP) test, this function tests a specifc region/gene by a GEE based minimum p-value test after fitting "null.LGRF()".

In this article, we proposed to apply the generalized Berk-Jones (GBJ) test and the generalized higher criticism (GHC) test to identify the genetic variants that affect multiple traits based on GWAS summary statistics.

minP test. Description. Return exact minP test p-value for multiple traits - single SNP association. Usage minP(Zi, r) Arguments