replicatesSpearmancor        package:RNAither        R Documentation

_C_o_m_p_u_t_e _t_h_e _c_o_r_r_e_l_a_t_i_o_n _c_o_e_f_f_i_c_i_e_n_t _b_e_t_w_e_n_n _r_e_p_l_i_c_a_t_e_s _o_r _e_x_p_e_r_i_m_e_n_t_s

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

     Computes Spearman's rank correlation coefficient for each
     replicate - either inside each experiment, or between experiments.

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

     replicatesSpearmancor(header, dataset, flag, col4val, col4anno, fileNameSuffix)

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

  header: the header of a dataset file generated with
          'generateDatasetFile' 

 dataset: an R data frame generated with 'generateDatasetFile' 

    flag: 1 or 2. 1 will compute the coefficient for a maximum of 3
          replicates, for each experiment available in the dataset. 2
          will summarize the replicates from each experiment with their
          root mean square and compute the correlation coefficient
          between experiments. 

 col4val: a character string specifying the column whose values will be
          used to compute the correlation coefficient 

col4anno: a character string specifying the name of the dataset column
          to be used to define the replicate, e.g. ' "GeneName"' or '
          "Internal_GeneID"' 

fileNameSuffix: a character string that will be used to name the output
          file containing a table with the correlation coefficients. 

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

     For ' flag==1', the correlation coefficients are printed out to
     the shell and saved in a text file named after the experiment name
     specified in the header concatenated with the character string
     filenamesuffix and "Spearmancor.txt".

     For ' flag==2', the correlation coefficients are printed out to
     the shell and saved in a text file named after the experiment name
     specified in the header concatenated with the character string
     filenamesuffix and "Spearmancor_AllExp.txt".

     The function returns a table containing the correlation
     coefficients.

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

     data(exampleHeader, package="RNAither")
     data(exampleDataset, package="RNAither")

     replicatesSpearmancor(header, dataset, 1, "SigIntensity", "GeneName", "testfile1_")

