intCor               package:MergeMaid               R Documentation

_C_o_r_r_e_l_a_t_i_o_n _o_f _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 the study specific
     correlation matrices, and, for each gene, the correlation of
     correlations.

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

        intCor(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.

     ...: Not implemented at this time

_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 output is an object of class  mergeCor.

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

     'mergeCor-class','intcorDens'

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

       
       data(mergeData)
       merged  <-mergeExprs(sample1,sample2,sample3)
       corcor  <-intCor(merged,method="spearman")
       plot(corcor)
       hist(corcor)

       vv<-c(1,3)
       corcor1  <-intCor(merged[vv],method="kendall")
       plot(corcor1,xlab="study A",ylab="study B",main="CORRELATION OF CORRELATION",col=3,pch=4)
       hist(corcor1,xlab="CORRELATION OF CORRELATION")
       

