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

Value

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

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(maanova)

Attaching package: 'maanova'

The following object is masked from 'package:base':

    norm

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/maanova/adjPval.Rd_%03d_medium.png", width=480, height=480)
> ### Name: adjPval
> ### Title: Generate FDR adjusted P values for F test result.
> ### Aliases: adjPval
> ### Keywords: utilities
> 
> ### ** Examples
> 
> data(abf1)
> ## Not run: 
> ##D  
> ##D fit.full.simple = fitmaanova(abf1,formula = ~Strain)
> ##D # F-test strain effect
> ##D ftest.all = matest(abf1, fit.full.simple, term="Strain",n.perm= 1000)
> ##D # make FDR adjusted P values
> ##D ftest.all = adjPval(ftest.all, 'jsFDR')
> ##D # there will be new fields in test.strain.fix after this
> ## End(Not run)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>