SKAT.SSD.All {SKAT}R Documentation

SNP-set 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


[Package SKAT version 1.3.2.1 Index]