qqnorm-methods             package:DEDS             R Documentation

_N_o_r_m_a_l _Q-_Q _P_l_o_t _f_o_r _D_E_D_S _O_b_j_e_c_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     The function 'qqnorm.DEDS' produces normal Quantile-Quantile plots
     of statistics for 'DEDS-class' objects. The points corresponding
     to genes with DEDS q- or adjusted p-values less than a user
     defined threshold are highlighted.

_U_s_a_g_e:

     ## S3 method for class 'DEDS':
     qqnorm(y, subset=c(1:nrow(y$stats)),
     xlab = "Quantiles of standard normal", thresh = 0.05, col = palette(), pch, ...)

_A_r_g_u_m_e_n_t_s:

       y: An object of 'DEDS', produced by 'deds.stat.linkC' or
          'deds.stat'.

  subset: A numeric vector indicating the subset of points to be
          plotted.

    xlab: A title for the x axis

  thresh: A numeric variable specifying the threshold of significance
          in differential expression (DE) for q- or  p-values of the
          DEDS object.

     col: A specificatio for the colors to be used for plotting. It
          should have a length bigger than two. The first is used for
          points with q- or adjusted p-values smaller than the
          specified threshould (group I) and the second for points with
          q- or adjusted p-values bigger than the threshould (group
          II).

     pch: A specification for the type of points to be used for
          plotting.  It should have a length bigger than two. The first
          parameter is used for group I genes, and the second for group
          II genes.

     ...: Extra parameters for plotting.

_D_e_t_a_i_l_s:

     The function 'qqnorm.DEDS' implements a S3 method of 'qqnorm' for
     'DEDS'. The 'DEDS' class is a simple list-based class to store
     DEDS results and 'qqnorm.DEDS' is used for a DEDS object that is
     created  by functions 'deds.stat', 'deds.stat.linkC'. The list
     contains a "stat" component, which stores statistics from various
     statistical tests. The function 'qqnorm.DEDS' extracts the "stat"
     component and produces a normal QQ plot for each type of
     statistics. 'qqnorm.DEDS' as a default highlights points
     (corresponding to genes) with DEDS adjusted p- or q-values less
     than a user defined threshold.

     For DEDS objects that are created by the function 'deds.pval', the
     "stat" matrix consists of unadjusted p-values from different
     statistical models. For graphical display of these p values, the
     user can use 'hist.DEDS' and 'pairs.DEDS'.

_A_u_t_h_o_r(_s):

     Yuanyuan Xiao, yxiao@itsa.ucsf.edu, 
      Jean Yee Hwa Yang, jean@biostat.ucsf.edu.

_S_e_e _A_l_s_o:

     'deds.stat', 'deds.pval', 'deds.stat.linkC', 'hist.DEDS',
     'qqnorm.DEDS'

_E_x_a_m_p_l_e_s:

     X <- matrix(rnorm(1000,0,0.5), nc=10)
     L <- rep(0:1,c(5,5))

     # genes 1-10 are differentially expressed
     X[1:10,6:10]<-X[1:10,6:10]+1
     # DEDS summarizing t, fc and sam
     d <- deds.stat.linkC(X, L, B=200)

     # qqnorm for t, fc and sam
     qqnorm(d)
     # change points color
     qqnorm(d, col=c(2,3))
     # change points type
     qqnorm(d, pch=c(1,2))

