Resampling_FWER: Obtain significant SNP sets after controlling family wise...

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

Description

Obtain significant SNP sets after controlling for family wise error rate (FWER) using resampled residuals. To use it, SKAT_Null_Model or SKAT_Null_Model_MomentAdjust should have n.Resampling > 0.

Usage

	Resampling_FWER(obj,FWER=0.05)

	Resampling_FWER_1(P.value, P.value.Resampling, FWER=0.05)

 

Arguments

obj	object returned from SKAT.SSD.All function.
P.value	a vector of SKAT p-values. If 100 genes were tested, this vector should have 100 p-values.
P.value.Resampling	a matrix of p-values of the resampled residuals. Each row represents each gene/snp set, and each column represents resampling set. For example, if you have 100 genes, and conducted resampling 1000 times ( ex.n.Resampling=1000 in SKAT_Null_Model), then it should be a 100 x 1000 matrix.
FWER	a numeric value of FWER rate to control (default=0.05)

Value

results	If you use the returned object from SKAT.SSD.all function, it is a sub-table of significant snp sets of the result table in the obj. If you use P.value and P.value.Resampling, it is a vector of significant p-values. If there is no significant snp set, it is NULL.
n	a numeric value of the number of significant snp sets.
ID	a vector of indexes of significant snp sets.

Author(s)

Seunggeun Lee

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