IsoTestBH              package:IsoGene              R Documentation

_T_e_s_t _o_f _m_o_n_o_t_o_n_i_c _t_r_e_n_d_s _u_s_i_n_g _t_h_e _f_i_v_e _t_e_s_t _s_t_a_t_i_s_t_i_c_s _w_i_t_h _B_H _o_r _B_Y _a_d_j_u_s_t_m_e_n_t

_D_e_s_c_r_i_p_t_i_o_n:

     The function adjusts for the raw p-values of the five test
     statistics using BH or BY procedure.

_U_s_a_g_e:

     IsoTestBH(rp, FDR, type = c("BH", "BY"), stat = c("E2",
     "Williams", "Marcus", "M", "ModifM"))

_A_r_g_u_m_e_n_t_s:

      rp: raw p-value matrix with each row for one gene and 6 columns,
          the first column contains the Probe.ID, the second to the
          sixth columns are raw p-values for the five test statistics

     FDR: the desired FDR to control

    type: choose BH or BY procedure to control FDR

    stat: choose one of the five test statistics to use

_D_e_t_a_i_l_s:

     The input raw p-values to this function can be the one sided or
     the two sided ones which are obtained using function raw.p. The
     results using one sided p-values and FDR controlling at alpha/2 is
     equivalent to that using two sided p-values and FDR controlling at
     alpha.

_V_a_l_u_e:

sign.genes: A list of significant genes while controlling FDR is
          obtained, with 4 columns: the first column is the probe ID,
          the second column is the row id, the third column is the raw
          p-values of the significant genes and the last column is the
          adjusted p-values of significant genes using BH or BY
          procedure

_N_o_t_e:

     This function only allows one type of FDR adjustment, either BH or
     BY. For other type of adjustment, see function 'mt.rawp2adjp' in
     package 'multtest'.

_A_u_t_h_o_r(_s):

     Lin et al.

_S_e_e _A_l_s_o:

     'mt.rawp2adjp', 'IsoRawp'

_E_x_a_m_p_l_e_s:

       set.seed(1234)
       rp <- data.frame(paste("g",1:100), matrix(runif(500,0,0.1), 100, 5))
       sign <- IsoTestBH(rp, FDR = 0.05, type = "BH", stat = "E2")

