Several Local False Discovery Rate Estimators

Share:

Description

Suite of R functions for the estimation of local false discovery rate (LFDR) using different methods.

Details

Package: PsiHat
Type: Package
Version: 1.0
Date: 2015-09-30
License: GPL-3
Depends: R (>= 2.14.0), methods, qvalue, splines
URL: http://www.r-project.org, http://www.bioconductor.org, http://www.statomics.com

Author(s)

Code: David R. Bickel and M. Padilla (modifications).
Authors of included code from other R packages: Bradley Efron, Brit B. Turnbull, Balasubramanian Narasimhan (package: locfdr).
Documentation: Alaa Ali, Kyle Leckett, Marta Padilla.
Maintainer: M. Padilla <padilla.mpf@gmail.com>

References

Bickel, D. R. (2013). Simple estimators of false discovery rates given as few as one or two p-values without strong parametric assumptions. Statistical Applications in Genetics and Molecular Biology, Statistical Applications in Genetics and Molecular Biology, 12(4), pp. 529-43.

Padilla, M., & Bickel, D. R. (2012). Estimators of the local false discovery rate designed for small numbers of tests. Statistical Applications in Genetics and Molecular Biology, 11(5), art. 4.

See Also

R packages: qvalue and locfdr (v1.1.7).

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
# a vector of p-values with missing elements:
y <- runif(55); y[c(13, 2,5)] <- NA

z1 <- lfdr.bbe1(pvalue = y, monotonic = TRUE)
z2 <- lfdr.bbe1(pvalue = y, robust = TRUE)
z3 <- lfdr.bbe(pvalue = y)
z4 <- rvalue(pvalue = y)
z8 <- lfdr.assumedNull(pvalue=y,plot=0,df=3)

# a statistic vector with missing elements:
y <- runif(55, -1, 5); y[c(13, 2,5)] <- NA

z5 <- lfdr.empiricalNull(stat = y, plot = 0, df = 3)
z6 <- lfdr.assumedNull(stat = y, plot = 0, df = 5)
z7 <- lfdr.elfdr(stat = y, plot = 0, df = 6)