readNimblegen             package:Ringo             R Documentation

_F_u_n_c_t_i_o_n _t_o _r_e_a_d _i_n _N_i_m_b_l_e_g_e_n _I_n_t_e_n_s_i_t_y _T_e_x_t _F_i_l_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Function to read in Nimblegen Intensity Text Files into an
     'RGList'. Calls some other functions for actual reading of data.
     This function is to be used with two-color NimbleGen array data.
     Use the function 'read.xysfiles' of the 'oligo' package for
     single-color data.

_U_s_a_g_e:

     readNimblegen(hybesFile, spotTypesFile, path = getwd(),
      headerPattern="# software=NimbleScan",verbose = TRUE, ...)

_A_r_g_u_m_e_n_t_s:

hybesFile: Name of the file describing the arrays. In 'limma' this file
          would be called targets file.

spotTypesFile: spot types also used by 'limma'

    path: Path to directoy that hold the files 'hybesFile',
          'spotTypesFile' and also the intensity files. Set this to
          'NULL' if you prefer the arguments 'hybesFile',
          'spotTypesFile' and the file-name entries of the hybes file
          to  be treated as absolute or relative file paths themselves.

headerPattern: string; pattern used to identify explantory header lines
          in the supplied pair-format files

 verbose: logical; progress output to STDOUT?

     ...: further arguments passed on the 'readNgIntensitiesTxt'

_V_a_l_u_e:

     Returns raw intensity values in form of an 'RGList'.

_A_u_t_h_o_r(_s):

     Joern Toedling toedling@ebi.ac.uk

_S_e_e _A_l_s_o:

     'rglist', 'readTargets'

_E_x_a_m_p_l_e_s:

       exDir <- system.file("exData",package="Ringo")
       exRG <- readNimblegen("example_targets.txt","spottypes.txt",path=exDir)
       print(exRG)

