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Last data update: 2014.03.03

R: Proportion of true null p-values

pi0est

R Documentation

Proportion of true null p-values

Description

Estimates the proportion of true null p-values, i.e., those following the Uniform(0,1) distribution.

Usage

pi0est(p, lambda = seq(0.05, 0.95, 0.05), pi0.method = c("smoother",
  "bootstrap"), smooth.df = 3, smooth.log.pi0 = FALSE, ...)

Arguments

`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 `pi0.method` = "smoother", pi_0 will be estimated by applying a smoother to a scatterplot of log(pi_0) estimates against the tuning parameter lambda. Optional.
`...`	Arguments passed from `qvalue` function.

Details

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.

Value

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.lambda`.
`pi0.smooth`	A vector of fitted values from the smoother fit to the pi_0 estimates at each `lambda` value (pi0.method="bootstrap" returns NULL).

Author(s)

John D. Storey

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.

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

Examples

# 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)

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/pi0est.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pi0est
> ### Title: Proportion of true null p-values
> ### Aliases: pi0est
> ### Keywords: nulls pi0est, proportion true
> 
> ### ** Examples
> 
> # 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)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>