GenABEL (version 1.8-0)

VIFGC_ovdom: Genomic control for over-dominant model of inheritance using VIF

Description

This function estimates the corrected statistic using genomic control for the over-dominant model, using VIF. VIF coefficients are estimated by optimizing different error functions: regress, median and ks.test.

Usage

VIFGC_ovdom(data, p, method = "regress", n, index.filter = NULL, proportion = 1, clust = 0, vart0 = 0, tmp = 0, plot = TRUE, lmax = NULL, color = "red")

Arguments

data

Input vector of Chi square statistic

method

Function of error to be optimized. Can be "regress", "median" or "ks.test"

p

Input vector of allele frequencies

index.filter

Indexes for variables that will be use for analysis in data vector

n

size of the sample

proportion

The proportion of lowest P (Chi2) to be used when estimating the inflation factor Lambda for "regress" method only

plot

If TRUE, plot of lambda will be produced

lmax

The threshold for lambda for plotting (optional)

color

The color of the plot

clust

For developers only

vart0

For developers only

tmp

For developers only

Value

A list with elements

Zx

output vector corrected Chi square statistic

vv

output vector of VIF

exeps

output vector of exepsons (NA)

calrate

output vector of calrate

F

F

K

K

Examples

require(GenABEL.data)
data(ge03d2)
# truncate the data to make the example faster
ge03d2 <- ge03d2[seq(from=1,to=nids(ge03d2),by=2),seq(from=1,to=nsnps(ge03d2),by=3)]
qts <- mlreg(phdata(ge03d2)$dm2~1,data=ge03d2,gtmode = "overdominant")
chi2.1df <- results(qts)$chi2.1df
s <- summary(ge03d2)
freq <- s$Q.2
result <- VIFGC_ovdom(p=freq,method = "median",data=chi2.1df,n=nids(ge03d2))