Mfuzzgui                package:Mfuzz                R Documentation

_G_r_a_p_h_i_c_a_l _u_s_e_r _i_n_t_e_r_f_a_c_e _f_o_r _M_f_u_z_z _p_a_c_k_a_g_e

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

     The function 'Mfuzzgui' provides a graphical user interface for
     clustering of microarray data and visualisation of results. It is
     based on the functions of the Mfuzz package.

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

     Mfuzzgui()

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

     The function 'Mfuzzgui' launches a graphical user interface for
     the _Mfuzz_ package. It is based on Tk widgets using the R TclTk
     interface by Peter Dalgaard. It also employs some pre-made widgets
     from the tkWidgets Bioconductor-package by Jianhua Zhang for the
     selection of objects/files to be loaded. 

     Mfuzzgui provides a convenient interface to most functions of the
     Mfuzz package without restriction  of flexibility. An exception is
     the batch processes such as 'partcoeff' and 'cselection' routines
     which  are used for parameter selection in fuzzy c-means
     clustering of microarray data. These routines are  not included in
     Mfuzzgui. To select various parameters, the underlying Mfuzz
     routines may be applied.

     Usage of Mfuzzgui does not require assumes an pre-built 'exprSet'
     object but can be used with tab-delimited text files containing
     the gene expression data.  Note, however, that the clustering is
     based on the   the ordering of samples (arrays) as of the columns
     in the expression matrix of the 'exprSet' object or in the
     uploaded table, respectively.  Also, replicated arrays in the 
     expression matrix (or table)  are treated as independent by the
     'mfuzz' function and, thus, should be averagered prior to
     clustering.

     For a overview of the functionality of Mfuzzgui, please refer to
     the package vignette. For a description of the underlying
     functions, please refer to the 'Mfuzz' package.

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

     Mfuzzgui returns a tclObj object.

_N_o_t_e:

     The newest versions of 'Mfuzzgui' can be found at the Mfuzz
     webpage  (<URL:
     http://itb.biologie.hu-berlin.de/~futschik/software/R/Mfuzz>).

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

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

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


        1.  M.E. Futschik and B. Charlisle, Noise robust clustering of
           gene expression time-course data, *Journal of Bioinformatics
            and Computational Biology*, Vol. 3, No. 4, 965-988, 2005.

        2.  Cho RJ, Campbell MJ, Winzeler EA,  Steinmetz L, Conway A,
           Wodicka L, Wolfsberg TG,  Gabrielian  AE, Landsman D,
           Lockhart   DJ, Davis RW,  A genome-wide transcriptional
           analysis of the mitotic cell cycle, *Mol Cell*,(2):65-73,
           1998.

        3.  Mfuzz web-page: <URL:
           http://itb.biologie.hu-berlin.de/~futschik/software/R/Mfuzz>

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

     'mfuzz'

