SKAT: SKAT.SSD.All – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

SKAT.SSD.All

SNP-set Kernel Association Test

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

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

`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.

Please see SKAT or SKATBinary for details.

`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.

Seunggeun Lee

SNP-Set (Sequence) Kernel Association Test

v2.0.1

GPL (>= 2)

Authors

Seunggeun (Shawn) Lee and Zhangchen Zhao, with contributions from Larisa Miropolsky and Michael Wu

Initial release

2020-10-20