SKAT.SSD.All: SNP-set Kernel Association Test

In lin-lab/SKAT: SNP-Set (Sequence) Kernel Association Test

Description

Iteratively carry out association tests with phenotypes and SNP sets in SSD file.

Usage

	SKAT.SSD.All(SSD.INFO, obj, ..., obj.SNPWeight=NULL)
	
	SKATBinary.SSD.All(SSD.INFO, obj, ..., obj.SNPWeight=NULL)

 

Arguments

SSD.INFO	SSD_INFO object returned from Open_SSD.
obj	output object from SKAT_Null_Model.
...	further arguments to be passed to “SKAT” or “SKATBinary”.
obj.SNPWeight	output object from Read_SNP_WeightFile (default=NULL). If NULL, the beta weight with the “weights.beta” parameter will be used.

Details

Please see SKAT or SKATBinary for details.

Value

results	dataframe that contains SetID, p-values (P.value), the number of markers in the SNP sets (N.Marker.All), and the number of markers to test for an association after excluding non-polymorphic or high missing rates markers (N.Marker.Test). The output dataframe from SKATBinary.SSD.All have more columns for the method to compute p-values and the minimum achievable p-values (MAP).
P.value.Resampling	the matrix that contains p-values of resampled phenotypes.

Author(s)

Seunggeun Lee

lin-lab/SKAT documentation built on May 29, 2019, 3:41 a.m.