pamr.listgenes             package:pamr             R Documentation

_A _f_u_n_c_t_i_o_n _t_o _l_i_s_t _t_h_e _g_e_n_e_s _t_h_a_t _s_u_r_v_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 list the genes that survive the thresholding, from
     the nearest shrunken centroid classifier produced by pamr.train

_U_s_a_g_e:

     pamr.listgenes(fit, data, threshold, genenames=F)

_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

genenames: Include genenames in the list? If yes, they are taken from
          "data". Default is false (geneid is always included in the
          list).

_D_e_t_a_i_l_s:

     'pamr.listgenes' List the geneids, and standardized centroids for
     each class, for genes surviving at the given threshold.

_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,geneid=as.character(1:1000))
     mytrain <-   pamr.train(mydata)
     mycv <- pamr.cv(mytrain,mydata)
     pamr.listgenes(mytrain, mydata, threshold=1.6)
      

