VIFGC: Genomic control for various model of inheritance using VIF

In GenABEL: genome-wide SNP association analysis

Description

This function estimates corrected statistic using genomic control for different models (recessive, dominant, additive etc.), using VIF. VIF coefficients are estimated by optimizing different error functions: regress, median and ks.test.

Usage

  VIFGC(data, p, x, method = "regress", n,
    index.filter = NULL, proportion = 1, clust = 0,
    vart0 = 0, tmp = 0, CA = FALSE, p.table = 0,
    plot = TRUE, lmax = NULL, color = "red", F = NULL,
    K = NULL, type_of_plot = "plot", ladd = NULL)

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
x	Model of inheritance (0 for recessive,0.5 for additive, 1 for dominant, also it could be arbitrary)
index.filter	Indexes for variables that will be use for analysis in data vector
n	The 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
type_of_plot	For developers only
lmax	The threshold for lambda for plotting (optional)
color	The color of the plot
F	The estimation of F (optional)
K	The estimation of K (optional)
ladd	The estimation of lambda for additive model (optional)
clust	For developers only
vart0	For developers only
tmp	For developers only
CA	For developers only
p.table	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(dm2~sex,data=ge03d2,gtmode = "dominant")
chi2.1df <- results(qts)$chi2.1df
s <- summary(ge03d2)
freq <- s$Q.2
result <- VIFGC(p=freq,x=1,method = "median",CA=FALSE,data=chi2.1df,n=nids(ge03d2))

Example output

Loading required package: MASS
Loading required package: GenABEL.data

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