overlap                package:Mfuzz                R Documentation

_C_a_l_c_u_l_a_t_i_o_n _o_f _t_h_e _o_v_e_r_l_a_p _o_f _s_o_f_t _c_l_u_s_t_e_r_s

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

     This function calculates  the overlap of clusters produced by
     'mfuzz'.

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

     overlap(cl)

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

      cl: object of class _flclust_

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

     The function generates a matrix of the  normalised overlap of soft
     clusters. The overlap indicates the extent of "shared" genes
     between clusters. For a mathematical definiton of the overlap, see
     the vignette of the package or the reference below.

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

     Matthias E. Futschik  (<URL:
     http://itb.biologie.hu-berlin.de/~futschik>)

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

     M.E. Futschik and B. Charlisle, Noise robust clustering of gene
     expression time-course data, Journal of Bioinformatics and
     Computational Biology, 3 (4), 965-988, 2005

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

     if (interactive()){
     data(yeast)
     # Data pre-processing
     yeastF <- filter.NA(yeast)
     yeastF <- fill.NA(yeastF)
     yeastF <- standardise(yeastF)

     # Soft clustering and visualisation
     cl <- mfuzz(yeastF,c=20,m=1.25)
     mfuzz.plot(yeastF,cl=cl,mfrow=c(4,5))

     # Calculation of cluster overlap and visualisation 
     O <- overlap(cl)
     X11()
     Ptmp <- overlap.plot(cl,over=O,thres=0.05)
     }

