Description Usage Arguments Details Value Author(s) References See Also Examples
Estimate the q-values for a given set of p-values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant.
1 2 |
p |
A vector of p-values (only necessary input). |
fdr.level |
A level at which to control the FDR. Must be in (0,1]. Optional; if this is selected, a vector of TRUE and FALSE is returned that specifies whether each q-value is less than fdr.level or not. |
pfdr |
An indicator of whether it is desired to make the estimate more robust for small p-values and a direct finite sample estimate of pFDR – optional. |
lfdr.out |
If TRUE then local false discovery rates are returned. Default is TRUE. |
pi0 |
It is recommended to not input an estimate of pi0. Experienced users can use their own methodology to estimate the proportion of true nulls or set it equal to 1 for the BH procedure. |
... |
Additional arguments passed to |
The function pi0est
is called internally and calculates the estimate of pi_0,
the proportion of true null hypotheses. The function lfdr
is also called internally and
calculates the estimated local FDR values. Arguments for these functions can be included via ...
and
will be utilized in the internal calls made in qvalue
. See http://genomine.org/papers/Storey_FDR_2011.pdf
for a brief introduction to FDRs and q-values.
A list of object type "qvalue" containing:
call |
Function call. |
pi0 |
An estimate of the proportion of null p-values. |
qvalues |
A vector of the estimated q-values (the main quantity of interest). |
pvalues |
A vector of the original p-values. |
lfdr |
A vector of the estimated local FDR values. |
significant |
If fdr.level is specified, and indicator of whether the q-value fell below fdr.level (taking all such q-values to be significant controls FDR at level fdr.level). |
pi0.lambda |
An estimate of the proportion of null p-values at each lambda value (see vignette). |
lambda |
A vector of the lambda values utilized to obtain |
John D. Storey
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
pi0est
, lfdr
, summary.qvalue
,
plot.qvalue
, hist.qvalue
, write.qvalue
1 2 3 4 5 6 7 8 9 10 11 12 |
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.