ppPlot {ShotgunFunctionalizeR}R Documentation

Observed and theoretical p-value quantiles

Description

This function plots the observed and theoretical p-value quantiles.

Usage

ppPlot(stat, log.pvalues=TRUE, xlim=NULL, ylim=NULL, ...)

Arguments

stat results from any gene- or pathway-centric analysis performed in ShotgunFunctionalizeR
log.pvalues should the p-value be plotted on a logarithmic scale?
xlim x limit of the plot. A suitable value is calculated if omitted
ylim y limit of the plot. A suitable value is calculated if omitted
... additional arguments for qqplot

See Also

qqplot, trendPlot, trendPlot.family, trendPlot.category, groupPlot,groupPlot.family,groupPlot.category

Examples

## Not run: 
data(OceanCOG)
po.stat<-testGeneFamilies.regression(OceanCOG, covariates=c(10, 70, 130, 200, 500, 770, 4000), log.covariates=T)
ppPlot(po.stat)
## End(Not run)

[Package ShotgunFunctionalizeR version 1.0-2 Index]