snpStats (version 1.22.0)

qq.chisq: Quantile-quantile plot for chi-squared tests

Description

This function plots ranked observed chi-squared test statistics against the corresponding expected order statistics. It also estimates an inflation (or deflation) factor, lambda, by the ratio of the trimmed means of observed and expected values. This is useful for inspecting the results of whole-genome association studies for overdispersion due to population substructure and other sources of bias or confounding.

Usage

qq.chisq(x, df=1, x.max, main="QQ plot",  sub=paste("Expected distribution: chi-squared (",df," df)", sep=""),  xlab="Expected", ylab="Observed", conc=c(0.025, 0.975), overdisp=FALSE, trim=0.5,   slope.one=FALSE, slope.lambda=FALSE, pvals=FALSE, thin=c(0.25,50), oor.pch=24, col.shade="gray", ...)

Arguments

x

A vector of observed chi-squared test values

df

The degreees of freedom for the tests

x.max

If present, truncate the observed value (Y) axis at abs(x.max). If x.max is negative, the y-axis will extend to abs(x.max) even if the observed data do not

main

The main heading

sub

The subheading

xlab

x-axis label (default "Expected")

ylab

y-axis label (default "Observed")

conc

Lower and upper probability bounds for concentration band for the plot. Set this to NA to suppress this

overdisp

If TRUE, an overdispersion factor, lambda, will be estimated and used in calculating concentration band

trim

Quantile point for trimmed mean calculations for estimation of lambda. Default is to trim at the median

slope.one

Is a line of slope one to be superimpsed?

slope.lambda

Is a line of slope lambda to be superimposed?

pvals

Are P-values to be indicated on an axis drawn on the right-hand side of the plot?

thin

A pair of numbers indicating how points will be thinned before plotting (see Details). If NA, no thinning will be carried out

oor.pch

Observed values greater than x.max are plotted at x.max. This argument sets the plotting symbol to be used for out-of-range observations

col.shade

The colour with which the concentration band will be filled

...

Further graphical parameter settings to be passed to points()

Value

The function returns the number of tests, the number of values omitted from the plot (greater than x.max), and the estimated dispersion factor, lambda.

Details

To reduce plotting time and the size of plot files, the smallest observed and expected points are thinned so that only a reduced number of (approximately equally spaced) points are plotted. The precise behaviour is controlled by the parameter thin, whose value should be a pair of numbers. The first number must lie between 0 and 1 and sets the proportion of the X axis over which thinning is to be applied. The second number should be an integer and sets the maximum number of points to be plotted in this section. The "concentration band" for the plot is shown in grey. This region is defined by upper and lower probability bounds for each order statistic. The default is to use the 2.5 Note that this is not a simultaneous confidence region; the probability that the plot will stray outside the band at some point exceeds 95

When required, the dispersion factor is estimated by the ratio of the observed trimmed mean to its expected value under the chi-squared assumption.

References

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

See Also

single.snp.tests, snp.lhs.tests, snp.rhs.tests

Examples

## See example the single.snp.tests() function