gap (version 1.1-1)

gcontrol2: genomic control based on p values

Description

The function obtains 1-df $\chi^2$ 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 $\chi^2$ statstics.

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.

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

Value

• A list containing:
• x
  the expected $\chi^2$ statistics
• y
  the observed $\chi^2$ statistics
• lambda
  the inflation factor

References

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

Examples

x2 <- rchisq(100,1,.1)
p <- pchisq(x2,1,lower.tail=FALSE)
r <- gcontrol2(p)
print(r$lambda)