getKGMLurl             package:KEGGgraph             R Documentation

_G_e_t _K_G_M_L _f_i_l_e (_u_r_l) _w_i_t_h _K_E_G_G _P_A_T_H_W_A_Y _I_D _a_n_d (_o_p_t_i_o_n_a_l) _o_r_g_a_n_i_s_m

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

     The function simply returns the KGML file url given KEGG PATHWAY
     ID. If the KEGG PATHWAY ID contains no organism prefix, user can
     specify the 'organism' parameter. Otherwise the 'organism' option
     is ignored.

     retrieveKGML is a simple wrapper to getKGMLurl, which downloads
     the KGML file with 'download.file' in utils package.

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

     getKGMLurl(pathwayid, organism = "hsa")
     retrieveKGML(pathwayid, organism, destfile,method="wget", ...)

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

pathwayid: KEGG PATHWAY ID, e.g. 'hsa00020'

organism: three-alphabet organism code, if pathwayid contains the ocde
          this option is ignored

destfile: Destination file, to which the remote KGML file should be
          saved

  method: Method to be used for downloading files, passed to
          'download.file' function. Currently supports "internal",
          "wget" and "lynx"

     ...: Parameters passed to download.file

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

     The function 'getKGMLurl' takes the pathway identifier (can be in
     the form of 'hsa00020' or with 'pathway' prefix, for example
     'path:hsa00020'), and returns the url to download KGML file.

     The mapping between pathway identifier and pathway name can be
     found by KEGGPATHNAME2ID (or reversed mappings) in KEGG.db
     package. See vignette for example.

     'retrieveKGML' calls 'download.file' to download the KGML file
     from KEGG FTP remotely.

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

     KGML File URL of the given pathway.

_N_o_t_e:

     So far the function does not check the correctness of the
     'organism' prefix, it is the responsibility of the user to
     garantee the right spelling.

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

     Jitao David Zhang <URL: mailto:j.zhang@dkfz.de>

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

     getKGMLurl("hsa00020")
     getKGMLurl("path:hsa00020")
     getKGMLurl("00020",organism="hsa")

     ## NOT RUN
     tmp <- tempfile()
     retrieveKGML(pathwayid='00010', organism='cel', destfile=tmp, method="wget")

