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