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, fitcv=NULL, genenames=FALSE)

_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

   fitcv: Optional object, result of a call to pamr.cv

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. If fitcv
     is provided, the function also reports the average rank of the
     gene in the cross-validation folds, and the proportion of times 
     that the gene is chosen (at the given threshold) in the
     cross-validation folds.

_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:

     #generate some data
     set.seed(120)
     x <- matrix(rnorm(1000*20),ncol=20)
     y <- sample(c(1:4),size=20,replace=TRUE)

     mydata <- list(x=x,y=factor(y), geneid=as.character(1:nrow(x)), genenames=paste("g",as.character(1:nrow(x)),sep=""),)

     #train classifier
     mytrain<-   pamr.train(mydata)

     pamr.listgenes(mytrain, mydata, threshold=1.6)
      

