gcontrol2 {gap} | R Documentation |
genomic control based on p values
Description
genomic control based on p values
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
The function obtains 1-df 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
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.
Value
A list containing:
x the expected
statistics.
y the observed
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)