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

In GenABEL: genome-wide SNP association analysis

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

Author(s)

Yakov Tsepilov

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))

GenABEL documentation built on May 30, 2017, 3:36 a.m.