LL-class             package:AnnBuilder             R Documentation

_C_l_a_s_s "_L_L" _a _s_u_b-_c_l_a_s_s _o_f _p_u_b_R_e_p_o _t_o _h_a_n_d_l_e _d_a_t_a _f_r_o_m _L_o_c_u_s_L_i_n_k

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

     This class is a sub-class of pubRepo that is implemented
     specifically to parse data from LocusLink (ll_teml.gz)

_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("LL", ...)'. A
     constructor (LL) is available and should be used to instatiate
     objects of 'LL'

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


     '_s_r_c_U_r_l': Object of class '"character", from class "pubRepo"' a
          character string for the surce url where data will be
          downloaded/processed

     '_p_a_r_s_e_r': Object of class '"character", from class "pubRepo"'  a
          character string for the name of the file containing a
          segment of perl code with instructions on how the source data
          will be processed and output be generated

     '_b_a_s_e_F_i_l_e': Object of class '"character", from class "pubRepo"' a
          character string for the name of the file that contains data
          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) 

_E_x_t_e_n_d_s:

     Class '"pubRepo"', directly.

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

     No methods defined with class "LL" in the signature.

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

     Jianhua Zhang

_R_e_f_e_r_e_n_c_e_s:

     <URL: www.ncbi.nlm.nih.gov/LocusLink>

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

     'pubRepo-class'

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

     ## Not run: 
     # Parse a truncated version of LL_tmpl.gz from Bioconductor
     path <- file.path(.path.package("AnnBuilder"), "scripts")
     temp <- matrix(c("32469_f_at", "D90278", "32469_at", "L00693", "33825_at",
     "X68733", "35730_at", "X03350", "38912_at", "D90042", "38936_at",
     "M16652"), ncol = 2, byrow = TRUE)
     write.table(temp, "tempfile", sep = "\t", quote = FALSE,
     row.names = FALSE, col.names = FALSE)  
     ll <- LL(srcUrl =
     "http://www.bioconductor.org/datafiles/wwwsources/Tll_tmpl.gz",
     parser = file.path(path, "gbLLParser"), baseFile = "tempfile")
     data <- parseData(ll)
     unlink("tempfile")
     ## End(Not run)

