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 1.14.0 Index]