readpDataSlides          package:arrayMagic          R Documentation

_R_e_a_d_s _t_h_e _d_e_s_c_r_i_p_t_i_o_n _o_f _a_l_l _s_l_i_d_e_s _o_r _c_h_a_n_n_e_l_s

_D_e_s_c_r_i_p_t_i_o_n:

     The function reads the 'slideDescriptionFile', which contains all
     information row-wise for each slide/microarray or for each channel
     in a tab-deliminated text file. The file is read up to the first
     line containing solely "white space".

_U_s_a_g_e:

     readpDataSlides(slideDescriptionFile = "slideDescription.txt", loadPath = ".", deleteBlanks = TRUE, verbose = TRUE)

_A_r_g_u_m_e_n_t_s:

slideDescriptionFile: character string; required; default
          "slideDescription.txt". The first line of the file must
          contain all column names, in particular the column named
          "fileName" which contains image analyis result file names and
          possibly additionally a column which contains the slide
          names; cf. the arguments 'fileNameColumn' and
          'slideNameColumn' of 'readIntensities'. Note: Column names
          must not contain underlines or spaces. 

loadPath: character string; required; default: ".". The path is used to
          load the 'slideDescriptionFile'; note: "." refers to the
          working directory. 

deleteBlanks: logical; required; default: 'TRUE'. Any blank character
          is removed from the text body of the 'slideDescriptionFile'.
          Thus no item/name should contain spaces. 

 verbose: logical; required; default: 'TRUE' 

_V_a_l_u_e:

     'data.frame'

_A_u_t_h_o_r(_s):

     Andreas Buness <a.buness@dkfz.de>

_S_e_e _A_l_s_o:

     'readIntensities', 'processArrayData'

_E_x_a_m_p_l_e_s:

            LOADPATH <- file.path(.path.package("arrayMagic"), "extdata")
             SLIDEDESCRIPTIONFILE <- "slideDescription"
       
             resultObject <- readpDataSlides(
                                  loadPath=LOADPATH, 
                                  slideDescriptionFile=SLIDEDESCRIPTIONFILE
                       )
      

