BCXmotifs              package:biclust              R Documentation

_T_h_e _X_m_o_t_i_f_s _B_i_c_l_u_s_t_e_r _a_l_g_o_r_i_t_h_m

_D_e_s_c_r_i_p_t_i_o_n:

     Performs XMotifs Biclustering based on the framework by Murali and
     Kasif (2003). Searches for a submatrix where each row as a similar
     motif through all columns. The Algorihm needs a discret matrix to
     perform.

_U_s_a_g_e:

     ## S4 method for signature 'matrix, BCXmotifs':
     biclust(x, method=BCXmotifs(), ns=10, nd=10, sd=5, alpha=0.05, number=100)

_A_r_g_u_m_e_n_t_s:

       x: Data Matrix.

  method: Here BCXmotifs, to perform Xmotifs algorithm

      ns: Number of rows choosen.

      nd: Number of repetitions.

      sd: Sample size in repetitions.

   alpha: Scaling factor for column result.

  number: Number of bicluster to be found.

_V_a_l_u_e:

     Returns an object of class 'Biclust'.

_E_x_t_e_n_d_s:

     Class '"BiclustMethod"', directly.

_A_u_t_h_o_r(_s):

     Sebastian Kaiser  sebastian.kaiser@stat.uni-muenchen.de

_R_e_f_e_r_e_n_c_e_s:

     Murali, T. & Kasif, S.  Extracting Conserved Gene Expression
     Motifs from Gene Expression Data  Pacific Symposium on
     Biocomputing, sullivan.bu.edu,  2003, 8, 77-88

_S_e_e _A_l_s_o:

     'biclust', 'Biclust'

_E_x_a_m_p_l_e_s:

     data(BicatYeast)
     x<-discretize(BicatYeast)
     res <- biclust(x, method=BCXmotifs(), ns=20, nd=20, sd=5, alpha=0.01, number=10)
     res

