PRv9mers            package:arrayQuality            R Documentation

_P_r_i_n_t _R_u_n _Q_u_a_l_i_t_y _v_e_r_s_i_o_n _9_m_e_r_s

_D_e_s_c_r_i_p_t_i_o_n:

     Qualitative diagnostic plots looking at print-run quality.  This
     component examine the 9mers hybridizations.

_U_s_a_g_e:

     PRv9mers(fnames, path = ".", dev = "png", DEBUG = FALSE, prargs = NULL, samepr = TRUE, prname = "xMm", save = TRUE, ...)

_A_r_g_u_m_e_n_t_s:

  fnames: A "character" string naming the input files.

    path: A "character" string representing the data directory. By
          default this is set to the current working directory (".").

     dev: A "character" string naming the graphics device. This will
          take arguments "png", "jpeg" and "ps" only.

   DEBUG: If 'TRUE', debug statements are printed.

  prargs: A list with 4 components: Block, Row, Column and ncolumns.
          See Details for more information.

  samepr: If 'TRUE', we assume everything in the directory are from the
          same print-run.

  prname: A "character" string giving the name of the print-run.

    save: If `TRUE', the figures will be saved to files.

     ...: additional arguments

_D_e_t_a_i_l_s:

     The argument "prargs" is used to calculate the layout information
     about a print-run.  Components Block, Row and Columns denote the
     column names from the input data representing the print-tip
     location. The component "ncolumns" is an integer representing the
     number of print-tip columns in the data.  If the arguement is set
     to NULL, the the following default will be used. 
     list(Block="Block", Row="Row", Column="Column", ncolumns=4)

_V_a_l_u_e:

     Files of diagnostic plots and  excel files containings probe IDs
     of problematic probes.

_A_u_t_h_o_r(_s):

     Jean Yee Hwa Yang

_E_x_a_m_p_l_e_s:

     datadir <- system.file("gprQCData", package="arrayQuality")
     if (interactive())
     PRv9mers(fnames="12Mm250.gpr", path=datadir, prname="12Mm")

