maanova (version 1.42.0)

adjPval: 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.

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)