Plotting function for q-value object

Description

Graphical display of the q-value object

Usage

## S3 method for class 'qvalue'
plot(x, rng = c(0, 0.1), ...)

Arguments

Details

The function plot allows one to view several plots:

1. The estimated pi_0 versus the tuning parameter lambda.

2. The q-values versus the p-values.

3. The number of significant tests versus each q-value cutoff.

4. The number of expected false positives versus the number of significant tests.

This function makes four plots. The first is a plot of the estimate of pi_0 versus its tuning parameter lambda. In most cases, as lambda gets larger, the bias of the estimate decreases, yet the variance increases. Various methods exist for balancing this bias-variance trade-off (Storey 2002, Storey & Tibshirani 2003, Storey, Taylor & Siegmund 2004). Comparing your estimate of pi_0 to this plot allows one to guage its quality. The remaining three plots show how many tests are called significant and how many false positives to expect for each q-value cut-off. A thorough discussion of these plots can be found in Storey & Tibshirani (2003).

Value

Nothing of interest.

Author(s)

John D. Storey, Andrew J. Bass

References

Storey JD. (2002) A direct approach to false discovery rates. Journal of the Royal Statistical Society, Series B, 64: 479-498.
http://onlinelibrary.wiley.com/doi/10.1111/1467-9868.00346/abstract

Storey JD and Tibshirani R. (2003) Statistical significance for genome-wide experiments. Proceedings of the National Academy of Sciences, 100: 9440-9445.
http://www.pnas.org/content/100/16/9440.full

Storey JD. (2003) The positive false discovery rate: A Bayesian interpretation and the q-value. Annals of Statistics, 31: 2013-2035.
http://projecteuclid.org/DPubS/Repository/1.0/Disseminate?view=body&id=pdf_1&handle=euclid.aos/1074290335

Storey JD, Taylor JE, and Siegmund D. (2004) Strong control, conservative point estimation, and simultaneous conservative consistency of false discovery rates: A unified approach. Journal of the Royal Statistical Society, Series B, 66: 187-205.

Storey JD. (2011) False discovery rates. In International Encyclopedia of Statistical Science.
http://genomine.org/papers/Storey_FDR_2011.pdf
http://www.springer.com/statistics/book/978-3-642-04897-5

See Also

qvalue, write.qvalue, summary.qvalue

Examples

# import data
data(hedenfalk)
p <- hedenfalk$p
qobj <- qvalue(p)

plot(qobj, rng=c(0.0, 0.3))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(qvalue)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/qvalue/plot.qvalue.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot.qvalue
> ### Title: Plotting function for q-value object
> ### Aliases: plot, plot.qvalue
> ### Keywords: plot
> 
> ### ** Examples
> 
> # import data
> data(hedenfalk)
> p <- hedenfalk$p
> qobj <- qvalue(p)
> 
> plot(qobj, rng=c(0.0, 0.3))
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>