intcor               package:metaArray               R Documentation

_I_n_t_e_g_r_a_t_i_v_e _C_o_r_r_e_l_a_t_i_o_n _A_n_a_l_y_s_i_s

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

     This function calculates gene-specific reproducibility score based
     on Parmigiani et al. R implementation in MergeMaid (pairwise.cor)
     is a  very efficient function in that it calculates the
     correlation matrix only  once and collect appropriate elements for
     calculation of scores for each gene.  However, in case there are
     more than thousands of common genes across datasets,  the
     correlation matrix may overflow memory cells alloted to a session
     of R.  Therefore, a replacement to the function that remedies the
     storage problem by brute  force but fast computation in C is
     provided here.

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

       intcor(merged)

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

  merged: 'mergeExprSet' object that contains gene expression and class
          label with all datasets.

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

 avg.cor: A vector of gene-specific integrative correlation score

pair.cor: A matrix of correlations for each gene in every pair of two
          studies

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

     Debashis Ghosh <ghoshd@umich.edu>, Hyungwon Choi
     <hwchoi@umich.edu>

_R_e_f_e_r_e_n_c_e_s:

     Clinical Cancer Research, Parmigiani et al. 10(9):2922-2927, 2004

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

      #intcor(merged)

