cMapPathBuilder          package:AnnBuilder          R Documentation

_F_u_n_c_t_i_o_n_s _t_h_a_t _b_u_i_l_d _a _d_a_t_a _p_a_c_a_k_g_e _u_s_i_n_g _d_a_t_a _p_r_o_v_i_d_e_d _b_y _c_M_A_P

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

     NCICB Pathway Interaction Database provides two data files
     molecule interaction data for BioCarta and KEGG pathways. The
     functions described here use the two files and build a data
     package containing the data

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

     cMapPathBuilder(cartaName, keggName, pkgName = "cMAP", pkgPath, version
     = "1.1.0", author = list(author = "anonymous", maintainer =
     "anonymous@email.com"))
     cMAPParser(sourceFile)  

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

cartaName: 'cartaName' a character string for the name of the XML file
          containing data for BioCarta pathways

keggName: 'keggName' a character string for the name of the XML file
          containing data for BioCarta pathways

 pkgName: 'pkgName' a character string for the name of the package to
          be built

 pkgPath: 'pkgPath' a character string for the path to the directory
          where the new package to built will reside

 version: 'version' a character string for the version number of
          package to be built

  author: 'author' a list with an author and maintainer element for the
          name and email address of the author of the pacakge

sourceFile: 'sourceFile' a character string for the name of the source
          data for BioCarta or KEGG

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

     cMAP currently does not support ftp downloading of the source data
     file. The files to be used have to be downloaded through a web
     browser and the name (with full path) of the downloaded file will
     be used.

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

     cMapPathBuilder returns a list with three elements: 

molecule: a list of vectors/lists containing molecule data

interaction: a list of vectors/lists containing molecule interaction
          data

 pathway: a list of vectors containing pathway component data

_N_o_t_e:

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

     Jianhua Zhang

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

     <URL: http://cmap.nci.nih.gov/PW/>

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

     ## No example is provided

