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

Description Usage Arguments Value Author(s)

View source: R/Function_Power_Resampling.R

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

1
2
3
4
5
	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.