maanova (version 1.42.0)

summarytable: Summarize the matest result.

Description

This function returns list of probe ID with p-value, FDR adjusted p-value or fold change selected by given threshold.

Usage

summarytable(matestobj, method=c("Fold.change","Pvalperm","adjPvalperm"),  test =c("F1","Fs"),whichTest=c("F1.Pvalperm","F1.adjPvalperm",  "Fs.Pvalperm","Fs.adjPvalperm"),  threshold, outfile="summarytable.csv")

Arguments

matestobj

An object of class matest, which is the result from matest.

method

Results that you want to include in the output among Fold.change, Pvalperm and adjPvalperm. Default is possible every field.

test

Test that you want to include in the output among F1, Fs and Fss. Default is possible every test.

whichTest

Test result used to get the subset. If whichTest is not provided, save all result.

threshold

Threshold that you want to get the subset. If threshold is not provided, save all result.

outfile

File name that you want to save the result. Default name is 'summarytable.csv'

Value

result

It returns result fields (among Fold.change, P-value or adjust P-value if you selected) from test statistics (among F1, Fs or Fss statistics if you selected), subsetted by given statistics ('whichtest') is smaller than 'threshold'.

outfile

.csv file saved under the working directory.

Details

This function use

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')
# summarytable(ftest.all, outfile='all.csv')
# smallset = summarytable(ftest.all, method ='Pvalperm',
# test=c('F1','Fs'), whichTest='Fs.Pvalperm', threshold = 0.1)
# ## End(Not run)