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)
)
```

- 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()

estimate of a, the number of alternative hypotheses

Other FDR:
`fdr()`

,
`fdr.master()`

,
`fdrBasic()`

,
`storey()`

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