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

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 1.2.1 Index]