updateSymbolsToValidKeys      package:annotate      R Documentation

_T_a_k_e _a _l_i_s_t _o_f _s_y_m_b_o_l_s _a_n_d _t_r_a_n_s_l_a_t_e _t_h_e_m _i_n_t_o _t_h_e _b_e_s_t _p_o_s_s_i_b_l_e
_I_D _f_o_r _a _p_a_c_k_a_g_e.

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

     Given a list of gene symbols and a package, find a valid ID for
     that package.  If there isn't a valid ID, then return the original
     symbol.

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

     updateSymbolsToValidKeys(symbols, pkg)

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

 symbols: A character vector containing gene symbols that you wish to
          try and translate into valid IDs.

     pkg: The package name of the chip for which we wish to validate
          IDs.

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

     This is a convenience function for getting from a possibly varied
     list of gene symbols mapped onto something that is a nice concrete
     ID such as an entrez gene ID.  When such an ID cannot be found,
     the original symbol will come back to prevent the loss of any
     information.

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

     This function returns a vector of IDs corresponding to the symbols
     that were input.  If the symbols don't have a valid ID, then they
     come back instead.

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

     Marc Carlson

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

     'isValidKey'

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

     ## Not run: 
       ## one "bad" ID, one that can be mapped onto a valid ID, and a 3rd
       ## which already is a valid ID
       syms <- c("15S_rRNA_2","21S_rRNA_4","15S_rRNA")
       updateSymbolsToValidKeys(syms, "org.Sc.sgd")

       ## 3 symbols and a 4th that will NOT be valid
       syms <- c("MAPK11","P38B","FLJ45465", "altSymbol")
       updateSymbolsToValidKeys(syms, "org.Hs.eg")
     ## End(Not run)

