| twilight {twilight} | R Documentation |
The function performs the successive exclusion procedure (SEP) as described in Scheid and Spang (2004).
twilight(xin, lambda = NULL, B = 0, boot.ci = 0.95, clus = NULL, verbose = TRUE)
xin |
Numerical vector of u-values, 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. |
See vignette.
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.
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.
Stefanie Scheid http://www.molgen.mpg.de/~scheid
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.
data(exfdr) # twilight object created by twilight with B=1000 bootstraps plot(exfdr,which="fdr")