mapGeneInfo              package:marray              R Documentation

_C_r_e_a_t_i_n_g _U_R_L _s_t_r_i_n_g_s _f_o_r _e_x_t_e_r_n_a_l _d_a_t_a_b_a_s_e _l_i_n_k_s

_D_e_s_c_r_i_p_t_i_o_n:

     These functions are used with 'htmlPage'. The function
     'mapGeneInfo', takes all the arguments and generate a character
     matrix of two columns.  The first columns representing the name of
     the argument and the second columns represents the value of an
     argument.  The function 'widget.mapGeneInfo' allows the user to
     enter this information  interactively.

_U_s_a_g_e:

     mapGeneInfo(widget = FALSE, Gnames, Name = "pubmed", ID =
                      "genbank", ACC = "SMDacc", ...)
     widget.mapGeneInfo(Gnames) 

_A_r_g_u_m_e_n_t_s:

  widget: A logical value specifying if widgets should be used.

    Name: The external database for spot description, E.g. "pubmed".

      ID: The external database for spot ID, E.g. "operon", "Riken",
          "locuslink".

     ACC: The external database for gene accession number, E.g.
          "genebank".

  Gnames: An object of class 'matrix', 'data.frame' or 'marrayInfo'
          which contains  description of spotted probe sequences.

     ...: Other column names

_D_e_t_a_i_l_s:

     The function 'mapGeneInfo' generates a character matrix with the
     first column representing the column headings of "Gnames" and the
     second column representing the corresponding names in the list
     'URLstring'.  For example, if a particular column in "Gnames" with
     column names "ID" contains genebank accession number, then the
     function 'mapGeneInfo' generates a row containing "ID" in the
     first column and "genbank" in the second.  Examples are 'SFGL' and
     'UCBFGL'.

     'URLstring' is a list contains the URL to various external
     database, E.g. operon, Riken, genbank. 
      The current choices are:  "pubmed",  "locuslink",  "riken",  
     "SMDclid",    "SMDacc",    "operonh2",  "operonh1" , "operonm2", 
     "operonm1" and  "genbank" .   "SMDclid" and "SMDacc" are links to
     Stanford Microarray Databases.

_A_u_t_h_o_r(_s):

     Jean Yee Hwa Yang

_E_x_a_m_p_l_e_s:

      mapGeneInfo(ID="genebank", ll="locuslink")
      mapGeneInfo(ID="locuslink", Sample.ID="riken")