adjPval               package:maanova               R Documentation

_G_e_n_e_r_a_t_e _F_D_R _a_d_j_u_s_t_e_d _P _v_a_l_u_e_s _f_o_r _F _t_e_s_t _r_e_s_u_l_t.

_D_e_s_c_r_i_p_t_i_o_n:

     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.

_U_s_a_g_e:

     adjPval(matestobj, method=c("stepup","adaptive", "stepdown", "jsFDR"))

_A_r_g_u_m_e_n_t_s:

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

  method: The method for FDR control.

_V_a_l_u_e:

     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.

_A_u_t_h_o_r(_s):

     Hao Wu

_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')
     # there will be new fields in test.strain.fix after this
     ## End(Not run)

