Usage
qvalue(p, lambda=seq(0,0.90,0.05), pi0.method="smoother", fdr.level=NULL, robust=FALSE,
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
fdr.level
A level at which to control the FDR. Must be in (0,1]. Optional; if this is
selected, a vector of TRUE and FALSE is returned that specifies
whether each q-value is less than fdr.level or not.
robust
An indicator of whether it is desired to make the
estimate more robust for small p-values and a direct finite sample
estimate of pFDR. Optional.
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.