pQQ: QQ-plot with confidence intervals for a vector of p-values

Description

Produces a QQ-plot of p-values. The x-axis is -log10 of the expected p-values (under a null hypothesis of no effects), the y-axis is -log10 values of the actual p-values. A (pointwise) confidence interval can be drawn, and names of snps/genes corresponding to the most significant ones can be added.

Usage

pQQ(pvals, nlabs = 6, conf = 0.95, lim, mark = 0.05, ...)

Arguments

pvals

A vector of p-values.

nlabs

The number of (most significant) p-values to be labeled using names(pvals).

conf

The confidence level of the pointwise confidence band. The default is 0.95. The confidence intervals are computed under the assumption of the p-values being drawn independently from a uniform [0,1] distribution. To leave out the confidence interval, set this to FALSE.

lim

A vector of length 2 giving the plot limits (on a log10 scal, for instance c(0,4)). Plot limits are computed automatically. However, if other plot limits are desireable, they can be set using this argument.

mark

By default, the 0.05 significance level is marked by lines. Can be changed to a different value, or set to FALSE.

...

Other arguments passed on to the plotting function.

Value

No value is returned.

Details

The pvals argument should be a vector of p-values to be plotted. If the vector has names corresponding to marker (snp) names, the plot will label some of the most significant points with the marker names.

References

Gjessing HK and Lie RT. Case-parent triads: Estimating single- and double-dose effects of fetal and maternal disease gene haplotypes. Annals of Human Genetics (2006) 70, pp. 382-396. Web Site: http://folk.uib.no/gjessing/genetics/software/haplin/