pamr.geneplot              package:pamr              R Documentation

_A _f_u_n_c_t_i_o_n _t_o  _p_l_o_t _t_h_e _g_e_n_e_s _t_h_a_t _s_u_r_i_v_e _t_h_e _t_h_r_e_s_h_o_l_d_i_n_g
_f_r_o_m _t_h_e _n_e_a_r_e_s_t _s_h_r_u_n_k_e_n _c_e_n_t_r_o_i_d _c_l_a_s_s_i_f_i_e_r

_D_e_s_c_r_i_p_t_i_o_n:

     A function to plot the genes that survive the thresholding, from
     the nearest shrunken centroid classifier produced by pamr.train

_U_s_a_g_e:

     pamr.geneplot(fit, data, threshold)

_A_r_g_u_m_e_n_t_s:

     fit: The result of a call to pamr.train

    data: The input data.  In the same format as the input data for
          pamr.train

threshold: The desired threshold value

_D_e_t_a_i_l_s:

     'pamr.geneplot' Plots the raw gene expression for genes that
     survive the specified threshold. Plot is stratified by class. 
     Plot is set up to display only up to about 20 or 25 genes,
     otherwise it gets too crowded. Hence threshold should be chosen to
     yield at most about 20 or 25 genes.

_A_u_t_h_o_r(_s):

     Trevor Hastie, Robert Tibshirani, Balasubramanian Narasimhan, and
     Gilbert Chu

_R_e_f_e_r_e_n_c_e_s:

_E_x_a_m_p_l_e_s:

     set.seed(120)
     x <- matrix(rnorm(1000*20),ncol=20)
     y <- sample(c(1:4),size=20,replace=TRUE)
     mydata <- list(x=x,y=y)
     mytrain <-   pamr.train(mydata)
     pamr.geneplot(mytrain, mydata, threshold=1.6)
      

