pamr.from.excel             package:pamr             R Documentation

_A _f_u_n_c_t_i_o_n _t_o _r_e_a_d _i_n _a _t_e_x_t _f_i_l_e _s_a_v_e_d _f_r_o_m _E_x_c_e_l

_D_e_s_c_r_i_p_t_i_o_n:

     A function to read in a text file saved from Excel. The
     spreadsheet is assumed to be of the format used by the SAM
     program.

_U_s_a_g_e:

     pamr.from.excel(file, ncols, sample.labels = FALSE, batch.labels = FALSE) 

_A_r_g_u_m_e_n_t_s:

    file: Character name of a text file. This is assumed to be a
          tab-delimited text file saved from an excel spreadsheet from 
          "SAM".  The spreadsheet has one row of expression values per
          gene. In addition there is one information row and two
          information columns.  The first row has class labels for each
          of the samples. The first column had gene identifiers, and
          the second column has gene names. In the SAM program, for the
          multiclass option, the samples must be labelled 1,2,3 etc.
          Here we allow general labels, like "lymphoma", "colon cancer"
          etc  

   ncols: Number of columns in file

sample.labels: Optional argument. If true, "file" is assumed to have an
          additional row at the top, consisting of two blank cells
          followed by a sample labels for each of the columns. If
          available, these sample labels are used by various plotting
          routines.

batch.labels: Optional argument. If true, "file" is assumed to have an
          additional row at the top, consisting of two blank cells
          followed by a batch labels for each of the columns. If
          sample.labels=T as well, the row of batch labels are assumed
          to  come after the row of sample labels. The batch labels are
          used by the function pamr.batchadjust. 

_D_e_t_a_i_l_s:

     'pamr.from.excel' {Reads in the  text file "file", and creates an
     object with components x (the matrix of expression values), y- a
     vector of class labels for each sample, geneid- a vector of gene
     identifiers and genenames- a vector of gene names}

_V_a_l_u_e:

     A list with components 

       x: 

       y: 

  geneid: 

genenames: a vector of gene names

samplelabels: a vector of sample labels, if provided in "file"

batchlabels: a vector of batch labels, if provided in "file"

_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:

