intcorDens             package:MergeMaid             R Documentation

_p_l_o_t _o_f _d_e_n_s_i_t_y _f_u_n_c_t_i_o_n_s _o_f _i_n_t_e_g_r_a_t_i_v_e _c_o_r_r_e_l_a_t_i_o_n_s

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

     Given a mergeExprSet, this function calculates and plots the
     density function of the integrative correlations, as well as
     densities for two "null distributions" obtained by randomly
     permuting sample IDs.

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

        intcorDens(x,method= c("pearson", "kendall", "spearman"),...)

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

       x: Object of class mergeExprSet.

  method: Method used to calculate correlation coefficient.

     ...: graphical parameters to be passed to plot.

_D_e_t_a_i_l_s:

     Integrative correlation coefficients are calcualted as follows. 
     The first step is to identify the n genes common to all studies.
     Within each study, we calculate the correlation coefficient
     between gene g, and every other common gene.  This gives a vector
     of length n-1.  For a pair of studies, S1 and S2, we calculate the
     correlation of correlations for gene g.  When there are more than
     2 studies under consideration, all pairwise correlation of
     correlations are calculated and averaged.

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

     The value is null.  Returns a plot.

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

     'mergeCor-class','intCor','modelOutcome'

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

      
       data(mergeData)
       merged  <-mergeExprs(sample1,sample2,sample3)
       intcorDens(merged)

       intcorDens(merged,cex.legend=1.5)

       intcorDens(merged,lty=2)
       

