Display q-value object

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Description

Display summary information for a q-value object.

Usage

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## 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

object

A q-value object.

cuts

Vector of significance values to use for table (optional).

digits

Significant digits to display (optional).

...

Additional arguments; currently unused.

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

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# 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))