two.stage: A p-value procedure which controls the FDR for independent...
In mutoss: Unified multiple testing procedures

Description Usage Arguments Details Value Author(s) Examples

A p-value procedure which controls the FDR for independent test statistics.

1	two.stage(pValues, alpha)

`pValues`	A numeric vecor of p-values.
`alpha`	The FDR error rate to control.

In the Benjamini-Krieger-Yekutieli two-stage procedure the linear step-up procedure is used in stage one to estimate m0 which is re-plugged in a linear step-up. This procedure is more powerful then non-adaptive procedures, while still controlling the FDR. On the other hand, error control is not guaranteed under dependence in which case more conservative procedures should be used (e.g. BH).

A list containing:

`rejected`	A logical vector indicating which hypotheses are rejected
`criticalValues`	A numeric vector containing critical values used in the step-up-down test.
`adjPValues`	A numeric vector containing adjusted p-values.
`pi0`	An estimate of the proportion of true null hypotheses among all hypotheses (pi0=m0/m).
`errorControl`	A Mutoss S4 class of type `errorControl`, containing the type of error controlled by the function and the level `alpha`.