r2cluster                package:ctc                R Documentation

_W_r_i_t_e _t_o _C_l_u_s_t_e_r _f_i_l_e _f_o_r_m_a_t

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

     Converting data to Cluster format

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

     r2cluster(data,labels=FALSE,colname="ACC",description=FALSE,
               file="cluster.txt",dec='.')

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

    file: the path of the file

    data: a matrix (or data frame) which provides the data to put into
          the file

  labels: a logical value indicating whether we use the frist column as
          labels (ACC column in cluster file)

 colname: a character string indicating  what kind of objects are in
          each row. YORF, MCLID, CLID, ACC can be used: see details. 

description: a logical value indicating whether we use the second
          column as description (NAME column for cluster file)

     dec: the character used in the file for decimal points

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

     Software _Cluster_, made by _M. Eisen_ needs formatted input data
     like:


     ACC     NAME    GWEIGHT GORDER  V3      V4      V5
     EWEIGHT                         1       1       1
     gbk01   Gene1   1       1       0.9     0.4     1.4
     gbk02   Gene2   1       2       0.6     0.2     0.2
     gbk03   Gene3   1       3       1.6     1.1     0.9
     gbk04   Gene4   1       4       0.4     1       1

     First field of first line (i.e "ACC") is a special field, that
     tells program what kind of objects are in each row.

     Four special values are defined with web link (when visualize with
     TreeView):

        *  YORF <URL:
           http://genome-www.stanford.edu/cgi-bin/dbrun/SacchDB?find+Locus+%22UNIQID%22>

        *  MCLID <URL:
           http://genome.rtc.riken.go.jp/cgi-bin/getseq?g+R+UNIQID>

        *  CLID <URL:
           http://genome-www4.stanford.edu/cgi-bin/SMD/source/sourceRes\-ult?op\-tion=CloneID&criteria1=IMAGE:UNIQID&choice=cDNA>

        *  ACC <URL:
           http://genome-www4.stanford.edu/cgi-bin/SMD/source/sourceRes\-ult?op\-tion=Number&criteria=UNIQID&choice=cDNA>

     Line begining with 'EWEIGHT' gives weights for each column
     (variable). Column 'GWEIGHT' gives weights for each line
     (individuals).

_N_o_t_e:

     _Cluster_ is a program made by _M. Eisen_ that performs
     hierarchical clustering, K-means and SOM. 

     _Cluster_ is copyrighted.  To get or have information about
     _Cluster_: <URL: http://rana.lbl.gov/EisenSoftware.htm>

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

     Antoine Lucas, <URL: http://antoinelucas.free.fr/ctc>

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

     Antoine Lucas and Sylvain Jasson, _Using amap and ctc Packages for
     Huge Clustering_, R News, 2006, vol 6, issue 5 pages 58-60.

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

     'xcluster', 'r2xcluster', 'hclust'

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

     #    Create data
     set.seed(1)
     m <- matrix(rep(1,3*24),ncol=3)  
     m[9:16,3] <- 3 ; m[17:24,] <- 3    #create 3 groups
     m <- m+rnorm(24*3,0,0.5)           #add noise
     m <- floor(10*m)/10                #just one digits

     r2cluster(m)

