adjPval {maanova} | R Documentation

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

### Description

This function takes a result object from `matest` and calculate the FDR adjusted P values. The new P values will be appended to the input object as additional fields. It has four options; "stepup" (Hochberg and Benjamini, 1990), "adaptive" (Benjamini and Hochberg, 2000), "stepdown" (Westfall and Young, 1993) and "jsFDR" (Storey, 2002). "jsFDR" option uses 'qvalue' package by John Storey and user suppose to install 'qvalue' package before using this option. There is no default option, thus you need to specify one option.

### Usage

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

### 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

### Examples

    data(abf1)
    ## Not run:

    fit.full.simple = fitmaanova(abf1,formula = ~Strain)
    # F-test strain effect
    ftest.all = matest(abf1, fit.full.simple, term="Strain",n.perm= 1000)
    # make FDR adjusted P values
    ftest.all = adjPval(ftest.all, 'jsFDR')
    # there will be new fields in test.strain.fix after this
    ## End(Not run)

[Package maanova version 1.8.1 Index]