getKEGGIDNName          package:AnnBuilder          R Documentation

_F_u_n_c_t_i_o_n_s _t_o _g_e_t/_p_r_o_c_e_s_s _p_a_t_h_w_a_y _a_n_d _e_n_z_y_m_e _d_a_t_a _f_r_o_m _K_E_G_G

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

     These functions extract pathway and enzyme data from KEGG <URL:
     ftp://ftp.genome.ad.jp/pub/kegg/pathways>. The functions are used
     by 'KEGG-class'.

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

     getKEGGIDNName(object, exten = "/map\_title.tab")
     getKEGGOrgName(name)
     getLLPathMap(srcUrl, idNName, organism, fromWeb = TRUE)
     mapll2EC(id, srcUrl, organism, fromWeb, sep = "\t")
     parseEC(llNEC)

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

  srcUrl: 'srcUrl' a character string for the url where source data are
          available

  object: 'object' a KEGG object with the slots filled with correct
          values

   exten: 'exten' a character string for data file name as an extension

    name: 'name' a character string for the name of the organism of
          concern. "human", "mouse", and "rat" are the valid values for
          now

organism: 'organism' same as name

 idNName: 'idNName' a named vector normally obtained obtained by using
          function 'getKEGGIDNName'

     sep: 'sep' a character string for the separators used to separator
          entries in a file

   llNEC: 'llNEC' a line of tab separated character strings with the
          first character string being a LocusLink id and second being
          the mapping enzyme (EC) names

      id: 'id' a character string for the KEGG id used for different
          pathway files

 fromWeb: 'fromWeb' a boolean to indicate whether a source data file
          will be read from a web site or locally

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

     'getKEGGIDNName' read the data file "map_title.tab" from KEGG to
     obtain the mappings between KEGG ids and pathway names.

     'getKEGGOrgName' takes the name for an organism and returns a
     short verion of the name used by KEGG for that organism.

     'getLLPathMap' maps LocusLink ids to pathway and enzyme names for
     an organism using various data files from KEGG.

     'mapll2EC' maps LocusLink ids to enzyme (EC) names for a given
     pathway.

     'parseEC' extracts enzyme data from a line of tab separated
     character strings to map a LocusLink id to enzyme (EC) names.

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

     'getKEGGIDNName' returns a named vector with KEGG ids being the
     names and pathway names being values.

     'getKEGGOrgName' returns a character string.

     'getLLPathMap' returns a list of two elements named "llec" and
     "llpathname". Each element is a matrix with mappings between
     LocusLink ids to enzyme or pathway names.

     'mapll2EC' returns a matrix with the first column being LocusLink
     ids and second enzyme (EC) names.

     'parseEC' returns two elements vector with the first element being
     a LocusLink id and second being the mapping enzyme (EC) names.

_N_o_t_e:

     The functions are part of the Bioconductor project at Dana-Farber
     Cancer Institute to provide Bioinformatics functionalities through
     R

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

     Jianhua Zhang

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

     <URL: www.genome.ad.jp/kegg/>

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

     'KEGG-class'

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

     getKEGGOrgName("Homo sapiens")
     # This group of code needs a while to finish
     if(interactive()){
     # Url may change but was correct at the time of coding
     idNPath <- getKEGGIDNName(KEGG(organism = "Homo sapiens"))
     temp <- getLLPathMap("ftp://ftp.genome.ad.jp/pub/kegg/pathways",
     idNPath, "Homo sapiens")
     temp <- mapll2EC("00010", "ftp://ftp.genome.ad.jp/pub/kegg/pathways",
     "Homo sapiens", sep = "\t")
     }

