Display q-value object

Description

Display summary information for a q-value object.

Usage

## S3 method for class 'qvalue'
summary(object, cuts = c(1e-04, 0.001, 0.01, 0.025, 0.05,
  0.1, 1), digits = getOption("digits"), ...)

Arguments

Details

summary shows the original call, estimated proportion of true null hypotheses, and a table comparing the number of significant calls for the p-values, estimated q-values, and estimated local FDR values using a set of cutoffs given by cuts.

Value

Invisibly returns the original object.

Author(s)

John D. Storey, Andrew J. Bass, Alan Dabney

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.
http://onlinelibrary.wiley.com/doi/10.1111/j.1467-9868.2004.00439.x/abstract

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, plot.qvalue, write.qvalue

Examples

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

# get summary results from q-value object
qobj <- qvalue(p)
summary(qobj, cuts=c(0.01, 0.05))

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/summary.qvalue.Rd_%03d_medium.png", width=480, height=480)
> ### Name: summary.qvalue
> ### Title: Display q-value object
> ### Aliases: summary, summary.qvalue
> ### Keywords: summary
> 
> ### ** Examples
> 
> # import data
> data(hedenfalk)
> p <- hedenfalk$p
> 
> # get summary results from q-value object
> qobj <- qvalue(p)
> summary(qobj, cuts=c(0.01, 0.05))

Call:
qvalue(p = p)

pi0:	0.669926	

Cumulative number of significant calls:

          <0.01 <0.05
p-value     265   605
q-value       1   162
local FDR     3    85

> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>