CountPlot              package:GeneMeta              R Documentation

_P_l_o_t_s _f_o_r _M_e_t_a-_a_n_a_l_y_s_i_s _o_f _g_e_n_e _e_x_p_r_e_s_s_i_o_n _d_a_t_a.

_D_e_s_c_r_i_p_t_i_o_n:

     Plots for meta-analysis

_U_s_a_g_e:

     IDRplot(m,CombineExp=1:(length(grep("zSco_Ex",colnames(m)))),colPos="black",colNeg="red",pchPos="*",pchNeg="*",type="b",ylab="IDR",xlab="z threshold",...)
     CountPlot(kkk,cols,Score=c("FDR","zSco"),kindof=c("two.sided","pos","neg"),type="b",pch="*",ylab="Number of genes",xlab="FDR threshold",CombineExp=1:((ncol(m)-6)/2-1) ,...)

_A_r_g_u_m_e_n_t_s:

       m: result matrix of the function 'zScores'

    type: plot parameter

    ylab: plot parameter

    xlab: plot parameter

     pch: plot parameter

  colPos: color for positive z scores

  colNeg: color for negative z scores

  pchPos: symbol for positive z scores

  pchNeg: symbol for negative z scores

CombineExp: vector of integer- which experiments should be
          combined-default:all experiments

     kkk: result object of function zScoreFDR

    cols: vector of cols, one for each experiment, and one for the
          combination

   Score: should the FDR or the zScore be plotted

  kindof: "pos", "neg" or "two.sided"

     ...: additional plot parameter

_D_e_t_a_i_l_s:

     IDRplot produces a plot described in Choi et al.

_V_a_l_u_e:

_A_u_t_h_o_r(_s):

     M.Ruschhaupt

_R_e_f_e_r_e_n_c_e_s:

     Choi et al, Combining multiple microarray studies and modeling
     interstudy variation. Bioinformatics, 2003, i84-i90.

_E_x_a_m_p_l_e_s:

