map2LL              package:AnnBuilder              R Documentation

_A _f_u_n_c_t_i_o_n _t_h_a_t _m_a_p_s _L_o_c_u_s_L_i_n_k _i_d_s _t_o _o_t_h_e_r _p_u_b_l_i_c _r_e_p_o_s_i_t_o_r_y _i_d_s
_a_n_d _v_i_c_e _v_e_r_s_a

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

     This function uses data files provided by NCBI to create a data
     package that contains mappings between LocusLink ids and GO,
     RefSeq, and UniGene ids and vice versa

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

     map2LL(pkgPath, organism, version, author, url =
     "ftp://ftp.ncbi.nih.gov/refseq/LocusLink/")
     getExten(what)
     getOrgName(organism, what = c("scientific", "short"))
     getReverseMapping(data, sep = ";")
     getUrl4Org(organism)
     getFullIDName(ID)
     saveData2Env(data, fun = splitEntry, pkgName, pkgPath, envName)
     reverseMap4GO(data, sep = ";")

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

organism: 'organism' a character string for the name of the organism of
          interest

 pkgPath: 'pkgPath' a character string for the name of the directory
          where the created data package will be stored

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

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

     url: 'url' a character string for the url of NCBI's ftp site where
          source data are stored. Current value is <URL:
          ftp://ftp.ncbi.nih.gov/refseq/LocusLink/>

    what: 'what' a character string for the type of mapping source data
          (i. e. "go", "ug" ...) or description of organism
          name("scientific" or "short")

    data: 'data' a matrix to be processed

     sep: 'sep' a character string the separator used to separate data
          elements for a given entry

      ID: 'ID' a character string for the short name of a data source
          (e. g. LL for LocusLink)

 envName: 'envName' a character string for the name of the environment
          object to be stored in the data package to be created

     fun: 'fun' the name of an R function to be called to process a
          data set before storing the data to an environment object

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

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

     Three files namely loc2go, loc2ref, and loc2UG will be used to
     create the mappings. The files were in <URL:
     ftp://ftp.ncbi.nih.gov/refseq/LocusLink/> at the time of the
     writing. 'getExten' maintains names for the three files. Should
     any of the names been changed by the server, 'getExten' has to be
     modified.

     'getExten' and 'saveColSepData' are supporting functions to
     'map2LL'

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

     invisible

_N_o_t_e:

     This function is part of Bioconductor project at Dana-Farber
     Cancer Institute to provide bioinfomatics functionalities through
     R

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

     Jianhua Zhang

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

     <URL: http://www.ncbi.nlm.nih.gov/LocusLink/>

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

     # Please note that the example will take a while to finish
     if(interactive()){
       map2LL(pkgPath = tempdir(), version = "1.0.0", organism = "human",
     author = list(author = "who", maintainer = "who@email.com"))
     }

