mapGeneInfo           package:marrayTools           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 = "operon", ACC = "genbank", ...)
     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")

