stat.gnames               package:sma               R Documentation

_S_o_r_t _G_e_n_e_s _A_c_c_o_r_d_i_n_g _t_o _t_h_e _V_a_l_u_e _o_f _a _S_t_a_t_i_s_t_i_c

_D_e_s_c_r_i_p_t_i_o_n:

     Lists genes and corresponding statistics in decreasing order of
     the statistics. This function applies to any type of statistic,
     including log ratios, one and two-sample t-statistics, and
     F-statistics. Missing values are ignored, as in 'sort(...,
     na.last=NA)'.

_U_s_a_g_e:

     stat.gnames(x, gnames, crit=0.05)

_A_r_g_u_m_e_n_t_s:

       x: a numeric vector containing the statistics for each gene.
          Missing values (NAs) are allowed. 

  gnames: a character vector containing the gene names.

    crit: specifies the number of genes to be returned. If crit < 1,
          the crit*100% genes with the largest x values are listed. If
          crit >= 1, the crit genes with the largest x values are
          listed. 

_V_a_l_u_e:

     List containing the following components  

  gnames: gene names sorted in decreasing order of the statistics in x.

       t: statistics sorted in decreasing order.

_A_u_t_h_o_r(_s):

     Yee Hwa Yang, yeehwa@stat.berkeley.edu 
      Sandrine Dudoit, sandrine@stat.berkeley.edu

_S_e_e _A_l_s_o:

     'stat.t2', 'order', 'sort'.

_E_x_a_m_p_l_e_s:

     ## Calculating log ratio and performing a t test.
     data(MouseArray)
     ## mouse.setup <- init.grid()
     ## mouse.data <- init.data() ## see \emph{init.data}
     mouse.lratio <- stat.ma(mouse.data, mouse.setup)
     cl <- c(rep(1,3), rep(2,3))
     mouse.t2 <- stat.t2(mouse.lratio, cl)

     ## Looking at gene names
     ## Finding the top 10 t-statistics
     stat.gnames(abs(mouse.t2$t), mouse.gnames, crit=10)

     ## Finding the top 1
     stat.gnames(abs(mouse.t2$t), mouse.gnames, crit=0.01)

     ## Finding the 10 extreme M values in the first slide
     stat.gnames(abs(mouse.lratio$M[, 1]), mouse.gnames, crit=10)

