IsopvaluePlot            package:IsoGene            R Documentation

_P_l_o_t _o_f _p-_v_a_l_u_e_s _f_r_o_m _p_e_r_m_u_t_a_t_i_o_n_s _u_n_d_e_r _i_n_c_r_e_a_s_i_n_g _o_r _d_e_c_r_e_a_s_i_n_g _a_l_t_e_r_n_a_t_i_v_e_s

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

     The function calculates the p-values using permutations under
     increasing and decreasing ordered alternatives for one gene. The
     p-values (p^up and p^down) are obtained from the plot of null
     distribution and observed statistics.

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

     IsopvaluePlot(x, y, niter, stat = c("E2", "Williams", "Marcus", "M", "ModifM"))

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

       x: the dose levels 

       y: the gene expressions

   niter: the number of permutations to use

    stat: choose one of the five test statistics to use

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

     Plots of the null distribution and the observed test statistic
     under increasing and decreasing ordered alternatives.

_N_o_t_e:

     The function obtains the p-values under increasing and decreasing
     ordered alternatives for a single gene.

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

     Lin et al.

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

     'IsoGene1'

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

     x <- c(rep(1,3), rep(2,3), rep(3,3), rep(4,3))
     y <- c(rnorm(3,1,1), rnorm(3,2,1), rnorm(3,3,1), rnorm(3,4,1)) 

     IsopvaluePlot(x, y, niter = 1000, stat = "Williams")

