adjPval {maanova} | R Documentation

## Generate FDR adjusted P values for F test result.

### Description

This function takes a result object from `matest` and calcualte the FDR adjusted P values. The new P values will be appended to the input object as additional fields.

### Usage

    adjPval(matestobj, method=c("stepup","adaptive", "stepdown"))

### Arguments

`matestobj` | An object of class `matest`, which is the result from `matest`.
`method` | The method for FDR control.

### Value

An object of class `matest` with the following fields added for each F test:

`adjPtab` | FDR adjusted tabulated P values.
`adjPvalperm` | FDR adjusted permutation P values.

### Author(s)

Hao Wu hao@jax.org

### Examples

    data(paigen)
    paigen <- createData(paigen.raw, n.rep=2)
    model.noint.fix <- makeModel(data=paigen, formula=~Array+Dye+Spot+Strain+Diet)
    # F-test strain effect
    ## Not run:
    test.strain.fix <- matest(paigen, model.noint.fix, term="Strain", n.perm=100,
            shuffle.method="resid", test.method=rep(1,4))
    # make FDR adjusted P values
    test.strain.fix <- adjPval(test.strain.fix)
    ## End(Not run)
    # there will be new fields in test.strain.fix after this

[Package maanova version 1.0.0 Index]