R: Polynomial genomic control

PGC {GenABEL} | R Documentation

## Polynomial genomic control

### Description

This function estimates the genomic controls for different models and degrees of freedom, using polinomial function. Polinomial coefficients are estimated by optimizing different error functions: regress, median, ks.test or group regress.

### Usage

      PGC(data, method = "group_regress", p, df, pol.d = 3,
        plot = TRUE, index.filter = NULL, start.corr = FALSE,
        proportion = 1, n_quiantile = 5, title_name = "Lambda",
        type_of_plot = "plot", lmax = NULL, color = "red")

### Arguments

`data` | Input vector of Chi square statistic
`method` | Function of error to be optimized. Can be "regress", "median", "ks.test" or "group_regress"
`p` | Input vector of allele frequencies
`df` | Number of degrees of freedom
`pol.d` | The degree of polinomial function
`plot` | If TRUE, plot of lambda will be produced
`start.corr` | For regress method use it only when you want to make calculations faster
`index.filter` | Index of variables in data vector, that will be used in analysis if zero - all variables will be used
`proportion` | The proportion of lowest P (Chi2) to be used when estimating the inflation factor Lambda for "regress" method only
`n_quiantile` | The number of groups for "group_regress" method
`title_name` | The title name for plot
`type_of_plot` | For developers only
`lmax` | The threshold for lambda for plotting (optional)
`color` | The color of the plot

### Value

A list with elements

`data` | Output vector corrected Chi square statistic
`b` | Polinomial coefficients

### Author(s)

Yakov Tsepilov

### Examples

    require(GenABEL.data)
    data(ge03d2)
    ge03d2 <- ge03d2[seq(from=1,to=nids(ge03d2),by=2),seq(from=1,to=nsnps(ge03d2),by=3)]
    qts <- mlreg(dm2~1,data=ge03d2,gtmode = "additive")
    chi2.1df <- results(qts)$chi2.1df
    s <- summary(ge03d2)
    freq <- s$Q.2
    result=PGC(data=chi2.1df,method="median",p=freq,df=1, pol.d=2, plot=TRUE, lmax=1.1,start.corr=FALSE)

[Package GenABEL version 1.8-0 Index]