chrLocPkgBuilder         package:AnnBuilder         R Documentation

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_t_h_e _L_o_c_u_s_L_i_n_k _i_d_s

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

     This function uses data provided by UCSC to build a data package
     that contains mappings between LocusLink ids and chromosome
     numbers and the chromosomal location of genes represented by
     LocusLink ids on each chromosome

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

     chrLocPkgBuilder(pkgName = "humanCHRLOC", pkgPath, version, author,
     organism = "human", url = getSrcUrl("gp", organism))
     getChrNum(chr)

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

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

 pkgPath: 'pkgPath' a character string for 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

organism: 'organism' a character string for the organism who will be
          target of the mapping

     url: 'url' a character string of the url of UCSC ftp site where to
          file refLink.txt.gz and refGene.txt.gz are stored. The files
          will be used to produce the data package

     chr: 'chr' a character string for the chromosome number extracted
          from the source data

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

     The data package created mappes LocusLink ids to chromosomal
     locations. Mappings of other public data repository ids including
     Gene Ontology, RefSeq, and UniGene to LocusLink ids can be made
     available using 'map2LL'

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

     invisible

_N_o_t_e:

     This function is part of the Bioconductor project at Dana-Farber
     Cancer Institue 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:

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

     'map2LL'

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

     # Please note that the example will take a while to finish
     if(interactive()){
     chrLocPkgBuilder(pkgName = "humanCHRLOC", pkgPath = tempdir(),
     version = "1.0.1", author = list(author = "who", maintainer =
     "who@email.com"), organism = "human", url = getSrcUrl("gp", "human"))
     }

