summary.qvalue {qvalue} | R Documentation

## 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

`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

    # 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))

[Package qvalue version 2.20.0 Index]