prop.alt {unknown} | R Documentation |
This is an internal function that calculates an estimate of a, the proportion of alternative hypotheses, using one of several methods.
prop.alt(pvals,adjustment.method="mean",adjustment.args=list(edf.lower=0.8,num.steps=20))
pvals |
a vector of pvals on which to conduct the multiple testing. |
adjustment.method |
an optional character string indicating the method for increasing the power of the procedure by estimating the proportion of alternative p-values, one of "mean", the modified Storey estimator that we suggest in Ventura et al. (2004), "storey", the method of Storey (2002), or "two-stage", the iterative approach of Benjamini et al. (2001) |
adjustment.args |
a list giving the arguments to
adjustment.method :
for adjustment.method="mean" , specify edf.lower, the smallest
quantile at which to estimate a, and num.steps, the number of quantiles to
use - the approach uses the average of the Storey (2002) estimator
for the num.steps quantiles starting at edf.lower and finishing just
less than 1
for adjustment.method="storey" , specify edf.quantile, the quantile
at which to calculate the estimator
for adjustment.method="two-stage" , the method uses a standard FDR
approach to estimate which p-values are significant; this number is
the estimate of a; therefore the method requires specification of
qlevel, the proportion of false positives and fdr.method ('original'
or 'general'), the FDR method to be used. We do not recommend
'general' as this is very conservative and will underestimate a.
|
estimate of a, the number of alternative hypotheses
Chris Paciorek paciorek AT alumni.cmu.edu
see fdr
.
a <- prop.alt(pvals,adjustment.method="mean",adjustment.args=list(edf.lower=0.8,num.steps=20)) a <- prop.alt(pvals,adjustment.method="storey",adjustment.args=list(edf.quantile=0.8)) a <- prop.alt(pvals,adjustment.method="two-stage",adjustment.args=list(qlevel=0.05,fdr.method='original'))