Proportion of alternate hypotheses

This is an internal function that calculates an estimate of a, the proportion of alternative hypotheses, using one of several methods.

propAlt(
  pvals,
  adjustment.method = "mean",
  adjustment.args = list(edf.lower = 0.8, num.steps = 20)
)

Arguments

pvals

a vector of pvals on which to conduct the multiple testing

adjustment.method

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

arguments to adjustment.method; see propAlt() for description, but note that for "two-stage", qlevel and fdr.method are taken from the qlevel and method arguments to fdr()

Value

estimate of a, the number of alternative hypotheses

See also

Other FDR: fdr(), fdr.master(), fdrBasic(), storey()

Author

Chris Paciorek

Examples

if (FALSE) { # \dontrun{
a <- propAlt(pvals,adjustment.method="mean")
} # }