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

VIFGC_ovdom {GenABEL} | R Documentation

## 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

### 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))

[Package GenABEL version 1.8-0 Index]