summarytable: Summarize the matest result.

In maanova: Tools for analyzing Micro Array experiments

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'

Details

This function use

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.

Author(s)

Hyuna Yang

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)

maanova documentation built on Nov. 8, 2020, 8:21 p.m.