readCodelink            package:codelink            R Documentation

_R_e_a_d _C_o_d_e_l_i_n_k _B_i_o_a_r_r_a_y_s _D_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     Read data exported as text by Codelink Software. It reads values
     (normalized by Codelink Software or not) flags and information
     about probes.

_U_s_a_g_e:

         readCodelink(files=list.files(pattern="TXT"), sample.name=NULL,
             flag, dec=NULL, type="Spot",    preserve=FALSE, verbose=2,
             file.type="Codelink", check=TRUE, fix=FALSE)

_A_r_g_u_m_e_n_t_s:

   files: list of files to read.

sample.name: vector of same length as files with sample names.

    flag: list with values to assign based on Flag quality values.

     dec: character indicating the decimal character used in the files.

    type: character indicating which base value to read from files.

preserve: logical, if TRUE Bkgd_stdev slot is not removed (if present).

 verbose: numerical, set the level of information. Level 2 set as old
          behaviour. Level > 2 output some debug info.

file.type: exported file type, currently Codelink or XLS file formats
          supported.

   check: logical, check for probe order consistency.

     fix: logical, try to fix probe order consistency.

_V_a_l_u_e:

     An object of class "Codelink".

_A_u_t_h_o_r(_s):

     Diego Diez

_S_e_e _A_l_s_o:

     'read.table'

_E_x_a_m_p_l_e_s:

     ## Not run: 
         # reading default extension (TXT).
         data <- readCodelink()

         # specify a different one.
         files <- list.files(pattern = "txt")
         data <- readCodelink(files = files)

         # example.
         data(codelink.example)
     ## End(Not run)

