SKAT (version 2.2.5)

Get_Logistic_Weights: Get the logistic weight

Description

Get logistic weights from either a genotype matrix (Z) or a vector of minor allele frequncies (MAF). Users can apply this weights to SKAT by giving it as the ``weights'' parameter. The logistic weight gives equal weights to rare variants and nearly zero weight to common variants.

Usage

Get_Logistic_Weights(Z, par1=0.07, par2=150)

	Get_Logistic_Weights_MAF(MAF, par1=0.07, par2=150)

Value

A vector of the logistic weight.

Arguments

Z

a numeric genotype matrix with each row as a different individual and each column as a separate gene/snp. Each genotype should be coded as 0, 1, 2, and 9 for AA, Aa, aa, and missing, where A is a major allele and a is a minor allele.

MAF

a numeric vector of minor allele frequncies.

par1

a numeric value of the first parameter of the logistic weight (default= 0.07).

par2

a numeric value of the second parameter of the logistic weight(default= 150).

Author

Seunggeun Lee

Details

The formula for the weight is $$ weights = \frac{e^{(par1 - MAF) par2}}{1 + e^{(par1 - MAF) par2}}. $$

Examples

data(SKAT.example)


#############################################################
#	Compute the P-value of SKAT with the logistic Weight (par1=0.07, par2=150)

# Use logistic weight
Z<-SKAT.example$Z
obj<-SKAT_Null_Model(y.c ~ X, out_type="C", data=SKAT.example)
weights<-Get_Logistic_Weights(Z, par1=0.07, par2=150)
SKAT(Z, obj, kernel = "linear.weighted", weights=weights)$p.value

# Weights function
MAF<-colMeans(Z)/2
plot(MAF,weights)