Description Usage Arguments Details Value Author(s) References See Also Examples
Estimates the proportion of true null p-values, i.e., those following the Uniform(0,1) distribution.
1 2 |
p |
A vector of p-values (only necessary input). |
lambda |
The value of the tuning parameter to estimate pi_0. Must be in [0,1). Optional, see Storey (2002). |
pi0.method |
Either "smoother" or "bootstrap"; the method for automatically choosing tuning parameter in the estimation of pi_0, the proportion of true null hypotheses. |
smooth.df |
Number of degrees-of-freedom to use when estimating pi_0 with a smoother. Optional. |
smooth.log.pi0 |
If TRUE and |
... |
Arguments passed from |
If no options are selected, then the method used to estimate pi_0 is the smoother method described in Storey and Tibshirani (2003). The bootstrap method is described in Storey, Taylor & Siegmund (2004). A closed form solution of the bootstrap method is used in the package and is significantly faster.
Returns a list:
pi0 |
A numeric that is the estimated proportion of true null p-values. |
pi0.lambda |
A vector of the proportion of null values at the lambda values (see vignette). |
lambda |
A vector of lambda value(s) utilized in calculating |
pi0.smooth |
A vector of fitted values from the
smoother fit to the pi_0 estimates at each |
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.
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | # import data
data(hedenfalk)
p <- hedenfalk$p
# proportion of null p-values
nullRatio <- pi0est(p)
nullRatioS <- pi0est(p, lambda=seq(0.40, 0.95, 0.05), smooth.log.pi0="TRUE")
nullRatioM <- pi0est(p, pi0.method="bootstrap")
# check behavior of estimate over lambda
# also, pi0est arguments can be passed to qvalue
qobj = qvalue(p, lambda=seq(0.05, 0.95, 0.1), smooth.log.pi0="TRUE")
hist(qobj)
plot(qobj)
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