PeptideAtlasBuilder_DB      package:PAnnBuilder      R Documentation

_B_u_i_l_d _d_a_t_a _p_a_c_k_a_g_e _f_o_r _e_x_p_e_r_i_m_e_n_t_a_l_l_y _i_d_e_n_t_i_f_i_e_d _p_e_p_t_i_d_e_s

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

     This function creates a data package for peptides identified in a
     large  set of tandem mass spectrometry proteomics experiments.

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

     PeptideAtlasBuilder_DB(name = c("Human","Human Plasma","Saccharomyces cerevisiae",
                         "Drosophila Melanogaster","Mouse Plasma","Halobacterium"),
                         prefix, pkgPath, version, author) 

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

    name: a character string to indicate which organisms or important 
          sample groups will be built. 

  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:

     Build annotation data packages for peptides identified in a large
     set of  tandem mass spectrometry proteomics experiments. Data are
     from PeptideAtlas database: <URL: http://www.peptideatlas.org>,
     including high quality peptide  sequences, their locations
     relative to the protein start (CDS coordinates),  and peptide
     locations in chromosomal coordinates.

     'PeptideAtlasBuilder_DB' employes functions 
     'writePeptideAtlasData_DB' to parse and write data.

     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 "org.Hs.pep.db" for Human PeptideAtlas.
     if(interactive()){
         PeptideAtlasBuilder_DB(name = "Human",
                             prefix = "org.Hs.pep", pkgPath, version, author) 
     }

