HomoloGeneBuilder_DB       package:PAnnBuilder       R Documentation

_B_u_i_l_d _D_a_t_a _P_a_c_k_a_g_e_s _f_o_r _H_o_m_o_l_o_g _P_r_o_t_e_i_n _G_r_o_u_p

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

     This function creates a data package of homologs among the
     annotated genes  of several completely sequenced eukaryotic
     genomes from NCBI HomoloGene.

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

     HomoloGeneBuilder_DB(prefix, pkgPath, version, author)

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

  prefix: the prefix of the name of the data package to be built. (e.g.
           "hsaSP"). The name of builded package is prefix+".db". 

 pkgPath: a character string for the full path of an existing directory
          where the built backage will be stored.

 version: a character string for the version number.

  author: a list with named elements "authors" containing a character
          vector of author names and "maintainer" containing the
          complete character string for the maintainer field, for
          example, "Jane Doe <jdoe@doe.com>".

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

     'HomoloGeneBuilder_DB' employes functions 
     'writeHomoloGeneData_DB' to parse and write data. Only several
     completely sequenced eukaryotic genomes are involved:  Homo
     sapiens, Pan troglodytes, Canis lupus familiaris, Bos taurus,  Mus
     musculus, Rattus norvegicus, Gallus gallus, Danio rerio, 
     Drosophila melanogaster, Anopheles gambiae, Caenorhabditis
     elegans,  Schizosaccharomyces pombe, Saccharomyces cerevisiae,
     Kluyveromyces lactis, Eremothecium gossypii, Magnaporthe grisea,
     Neurospora crassa,  Arabidopsis thaliana, Oryza sativa, Plasmodium
     falciparum.

     Data files in the database will be automatically downloaded to the
     tmp directory, so enough space is needed for the data files. After
     downloading, files are parsed by perl, so perl must be installed. 
     It may  take a long time to parse database and build R package.
     Alternatively, we have  produced diverse R packages by
     PAnnBuilder, and you can download appropriate  package via <URL:
     http://www.biosino.org/PAnnBuilder>.

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

     This function does not return any value.

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

     Hong Li

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

     # Set path, version and author for the package.
     pkgPath <- tempdir()
     version <- "1.0.0"
     author <- list()
     author[["authors"]] <- "Hong Li"
     author[["maintainer"]] <- "Hong Li <sysptm@gmail.com>"

     ## It may take a long time to parse database and build R package.
     # Build annotation data packages "homolog.db" for Homo sapiens proteomics gene 
     # ontology.
     if(interactive()){
         HomoloGeneBuilder_DB(prefix = "homolog", pkgPath, version, author)
     }

