GESAT.SSD.All: Gene-Environment Set Association Test

In lin-lab/iSKAT-GESAT: interaction Sequence/SNP-set Kernel Association Test (iSKAT) / Gene-Environment Set Association Test (GESAT)

Description

Iteratively test for interactions between a set of SNPS/genes and Environment for SNP sets in SSD file.

Usage

	GESAT.SSD.All(SSD.INFO, ...)
 

Arguments

SSD.INFO	an SSD_INFO object returned from Open_SSD.
...	further arguments to be passed to “GESAT”.

Details

Returns a data frame, where each row gives pvalue, Is_converge, lambda, n.G.test, n.GE.test, Error for that particular SETID. Please see GESAT for details.

Value

SetID	SetID.
pvalue	the p-value of GESAT.
Is_Converge	an indicator of the convergence. 1 indicates the method converged, and 0 indicates the method did not converge. When Is_Converge=0 (no convergence), "liu" method is used to compute p-value. Note that if method="liu", Is_converge=1 always.
lambda	the chosen tuning parameter.
n.G.test	the number of SNPs in the genotype matrix used in the test. It can be different from ncol(Z) when some markers are monomorphic or have higher missing rates than the missing_cutoff.
n.GE.test	the number of columns in the ZxE interaction matrix used in the test. It can be different from ncol(Z)*ncol(E) when some markers are monomorphic or have higher missing rates than the missing_cutoff. It can also be different from n.G.test*ncol(E) as the resulting ZxE variable might have no variability or might be perfectly collinear with columns of Z. Note that singletons are adjusted for in the main effects but are not tested for interactions. Likewise, columns of ZxE perfectly collinear with columns of Z are not tested for interactions.
Error	1= Error, 0=No Error.

Author(s)

Xinyi (Cindy) Lin

lin-lab/iSKAT-GESAT documentation built on Oct. 7, 2019, 1:16 a.m.