R: genomic control based on p values

gcontrol2 {gap} | R Documentation

## genomic control based on p values

### Description

The function obtains 1-df chi-squared statistics (observed) according to a vector of p values, and the inflation factor (lambda) according to medians of the observed and expected statistics. The latter is based on the empirical distribution function (EDF) of 1-df chi-squared statstics.

### Usage

    gcontrol2(p, col = palette()[4], lcol = palette()[2], ...)

### Arguments

`p` | a vector of observed p values.
`col` | colour for points in the Q-Q plot.
`lcol` | colour for the diagonal line in the Q-Q plot.
`...` | other options for plot.

### Details

It would be appropriate for genetic association analysis as of 1-df Armitage trend test for case-control data; for 1-df additive model with continuous outcome one has to consider the compatibility with p values based on z-/t- statistics.

### Value

A list containing:

x

  the expected chi-squared statistics

y

  the observed chi-squared statistics

lambda

  the inflation factor

### Author(s)

Jing Hua Zhao

### References

Devlin B, Roeder K (1999) Genomic control for association studies. Biometrics 55:997-1004

### Examples

    ## Not run:
    x2 <- rchisq(100,1,.1)
    p <- pchisq(x2,1,lower.tail=FALSE)
    r <- gcontrol2(p)
    print(r$lambda)

    ## End(Not run)

[Package gap version 1.2.3-6 Index]