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

Resampling_FWER {SKAT} | R Documentation

## Obtain significant SNP sets after controlling family wise error rate (FWER)

### 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

[Package SKAT version 1.3.2.1 Index]