GP-class             package:AnnBuilder             R Documentation

_C_l_a_s_s "_G_P" _a _s_u_b-_c_l_a_s_s _o_f _p_u_b_R_e_p_o _t_o _g_e_t/_p_r_o_c_e_s_s _d_a_t_a _f_r_o_m _G_o_l_d_e_n_P_a_t_h

_D_e_s_c_r_i_p_t_i_o_n:

     This class is a sub-class of pubRepo with source specific
     functions to get/process data from GoldenPath {<URL:
     http://www.genome.ucsc.edu/goldenPath>} to obtain gene location
     and orientation data

_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("GP", ...)'. A
     constructor (GP) is available and should be used to instantiate
     objects of this class

_S_l_o_t_s:

     `_o_r_g_a_n_i_s_m': Object of class `"character", from class "UG"' s
          character string for the organism of concern

     `_s_r_c_U_r_l': Object of class `"character", from class "UG"' a
          character string for the url where the source data are. As
          multiple data sources will be used, srcUlr in this case is
          the location where the surce data are (e.g. <URL:
          http://www.genome.ucsc.edu/goldenPath/14nov2002/database/>)  

     `_p_a_r_s_e_r': Object of class `"character", from class "UG"' not in
          use

     `_b_a_s_e_F_i_l_e': Object of class `"character", from class "UG"' not in
          use

_E_x_t_e_n_d_s:

     Class `"UG"', directly. Class `"pubRepo"', by class "UG".

_M_e_t_h_o_d_s:

     _g_e_t_S_t_r_a_n_d `signature(object = "GP")': Processes the refLink and
          refGene data files and returns a matrix with gene location
          and orientation data

_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

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://www.genome.ucsc.edu>

_S_e_e _A_l_s_o:

     `pubRepo-class'

_E_x_a_m_p_l_e_s:

     # The example may take a few second to finish
     if(interactive()){
       # The url (\url{http://www.genome.ucsc.edu/goldenPath/14nov2002/database/})
       # was correct at the time of coding. Replace with a correct one if it
       # is invalid 
       url <- getSrcUrl("GP", organism = "human")
       gp <- GP(srcUrl = url, organism = "human")
       strand <- getStrand(gp)
     }