twilight {twilight}R Documentation

Estimation of local false discovery rate

Description

The function performs the successive exclusion procedure (SEP) as described in Scheid and Spang (2004).

Usage

twilight(xin, lambda = NULL, B = 0, boot.ci = 0.95, clus = NULL, verbose = TRUE)

Arguments

xin Numerical vector of p-values or a twilight object.
lambda Numerical value denoting the penalty factor. If not specified, the function searchs for an appropriate regularization parameter.
B Numerical value specifying the number of bootstrap samples. If not specified, no bootstrap estimates are calculated.
boot.ci Numerical value denoting the probability value for bootstrap confidence intervals of local false discovery rate and prior pi0.
clus A list or numerical value to be passed to makeCluster(clus,...) in library(snow). If specified, bootstrapping is performed in parallel. No checks on clus are performed. Please make sure that makeCluster(clus) works properly in your environment.
verbose Logical value for message printing.

Details

See vignette.

Value

Returns a twilight object consisting of a data.frame named result with variables

pvalue Sorted input vector.
qvalue q-values computed as described in Storey and Tibshirani (2003) with new estimate pi0.
index Index of the original ordering.
fdr Local false discovery rate averaged over 10 runs of SEP.
mean.fdr Bootstrap estimate of local false discovery rate.
lower.fdr Lower boot.ci-bootstrap confidence bound.
upper.fdr Upper boot.ci-bootstrap confidence bound.

Values are sorted by pvalue.

Note

Additional output consists of

lambda Regularization parameter.
pi0 SEP estimate of prior probability.
boot.pi0 Bootstrap estimate and boot.ci-bootstrap confidence bounds.
boot.ci Passes boot.ci for plotting.
effect Histogram of effect size distributions averaged over 10 runs of SEP.

If xin is of class twilight, the remaining slots are filled with corresponding input values. If xin is not of class twilight, these slots remain free.

Author(s)

Stefanie Scheid http://www.molgen.mpg.de/~scheid

References

Scheid S and Spang R (2004): A stochastic downhill search algorithm for estimating the local false discovery rate, IEEE TCBB 1(3), 98–108.

Storey JD and Tibshirani R (2003): Statistical significance for genomewide studies, PNAS 100(16), 9440–9445.

See Also

twilight.pval, plot.twilight, exfdr

Examples

data(exfdr) # twilight object created by twilight with B=1000 bootstraps
exfdr
plot(exfdr,which="fdr")

[Package twilight version 1.4.0 Index]