summarytable             package:maanova             R Documentation

_S_u_m_m_a_r_i_z_e _t_h_e _m_a_t_e_s_t _r_e_s_u_l_t.

_D_e_s_c_r_i_p_t_i_o_n:

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

_U_s_a_g_e:

     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")

_A_r_g_u_m_e_n_t_s:

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'

_D_e_t_a_i_l_s:

     This function use

_V_a_l_u_e:

  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.

_A_u_t_h_o_r(_s):

     Hyuna Yang

_E_x_a_m_p_l_e_s:

     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)

