plot.subex: Plotting the P-value, Q-values, and the Regression Surface

In pi0: Estimating the proportion of true null hypotheses for FDR

Description

This function plots the p-value, q-values, and the regression surface for an object of class subex, typically from calling the function subex.

Usage

## S3 method for class 'subex'
plot(x,y,rgl = TRUE,...)

Arguments

x	the subex object
y	the same as rgl. If not missing, it overrides rgl.
rgl	logical, specifying whether or not the rgl package is used for making better 3D interactive graphs.
...	other arguments to be passed to persp3d, or persp if rgl package is not available.

Details

Two plots will be generated. The first one is a histogram of p-values in the blue color. A horizontal blue line is added indicating the height of pi0, i.e., the proportion of true null hypotheses. This histogram is overlaid with a red line of FDRs, indicating the corresponding q-value for each p-value. The right most end, i.e., the q-value corresponding to a p-value of 1, is the also of height pi0.
The other plot is the same as the plot.extrpi0.

Value

an invisible(NULL), used for side effects only.

Note

Because this function will call plot.extrpi0, a warning will be generated when rgl package is not available.

Author(s)

Long Qu

References

Qu, L., Nettleton, D., Dekkers, J.C.M. Subsampling Based Bias Reduction in Estimating the Proportion of Differentially Expressed Genes from Microarray Data. Unpublished manuscript.

See Also

plot.extrpi0, rgl ,subex

Examples

## Not run: 
set.seed(9992722)
## this is how the 'simulatedDat' data set in this package generated
simulatedDat=sim.dat(G=5000)
## this is how the 'simulatedSubex' object in this package generated
simulatedSubex=subex(simulatedDat,balanced=FALSE,max.reps=Inf,plotit=FALSE)
plot(simulatedSubex)
plot(simulatedSubex,FALSE)

## End(Not run)

pi0 documentation built on May 2, 2019, 4:47 p.m.