pubRepo-class           package:AnnBuilder           R Documentation

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

     This class provides the basic functions to download/parser data
     from different public data repositories. More specific functions
     can be provided by extending this class to include source specific
     features

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("pubRepo", ...)'.
     A constructor ('pubRepo' is provided and should be used to create
     objects of this class.

_S_l_o_t_s:

     '_s_r_c_U_r_l': Object of class '"character"' a character string for the
          url of a data source from a public repository

     '_p_a_r_s_e_r': Object of class '"character"' a character string for the
          name of a file that will be used as part of perl script to
          parse the source data. Parser is a segment of perl code
          containing instructions on how the source data will be
          processed and the content and format of the output

     '_b_a_s_e_F_i_l_e': Object of class '"character"' a character string for
          the name of a file that will be used as the  base to process
          the source data. Data from the source that are related to
          elements in the base file will be extracted. baseFile is
          assumed to be a two folumn file with the first column being
          some type of arbitrary ids (e.g. Affymetrix probe ids) and
          the second cloumn being the corresponding ids of a given
          public repository (e.g. GenBank accession numbers or UniGene
          ids)

_M_e_t_h_o_d_s:

     _b_a_s_e_F_i_l_e<- 'signature(object = "pubRepo")': Sets the value for
          baseFile

     _b_a_s_e_F_i_l_e 'signature(object = "pubRepo")': Gets the value for
          baseFile

     _d_o_w_n_l_o_a_d_D_a_t_a 'signature(object = "pubRepo")': Downloads data from
          a data source defined by srcUrl

     _p_a_r_s_e_D_a_t_a 'signature(object = "pubRepo")': DownLoads/parses data
          from a data source defined by srcUrl

     _p_a_r_s_e_r<- 'signature(object = "pubRepo")': Sets the value for
          parser

     _p_a_r_s_e_r 'signature(object = "pubRepo")': Gets the value for parser

     _r_e_a_d_D_a_t_a 'signature(object = "pubRepo")': Reads data using
          'readLines' from a data source defined by srcUrl

     _s_r_c_U_r_l<- 'signature(object = "pubRepo")': Sets the value for
          srcUrl

     _s_r_c_U_r_l 'signature(object = "pubRepo")': Gets the value for srcUrl

_N_o_t_e:

     This class is part of the Bioconductor project at Dana-Farber
     Cancer Institute to provide Bioinformatics functionalities through
     R

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

     Jianhua Zhang

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

     'GO-class', 'KEGG-class', 'LL-class', 'UG-class', 'GEO-class'

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

     # Read a short test file from Bioconductor
     test <- pubRepo(srcUrl =
     "http://www.bioconductor.org/datafiles/wwwsources/TGene.txt")
     data <- readData(test)

