org.EcK12.egALIAS2EG     package:org.EcK12.eg.db     R Documentation

_M_a_p _b_e_t_w_e_e_n _C_o_m_m_o_n _G_e_n_e _S_y_m_b_o_l _I_d_e_n_t_i_f_i_e_r_s _a_n_d _E_n_t_r_e_z _G_e_n_e

_D_e_s_c_r_i_p_t_i_o_n:

     org.EcK12.egALIAS is an R object that provides mappings between
     common gene symbol identifiers and entrez gene identifiers.

_D_e_t_a_i_l_s:

     Each gene symbol maps to a named vector containing the
     corresponding entrez gene  identifier. The name of the vector
     corresponds to the gene symbol.  Since gene  symbols are sometimes
     redundantly assigned in the literature, users are cautioned  that
     this map may produce multiple matching results for a single gene
     symbol.  Users  should map back from the entrez gene IDs produced
     to determine which result is the  one they want when this happens.

     Because of this problem with  redundant assigment of gene symbols,
     is it never  advisable to use gene symbols as primary identifiers.       

     This mapping includes ALL gene symbols including those which are
     already listed  in the SYMBOL map.  The SYMBOL map is meant to
     only list official gene symbols,  while the ALIAS maps are meant
     to store all used symbols.

     Mappings were based on data provided by: Entrez Gene (
     ftp://ftp.ncbi.nlm.nih.gov/gene/DATA ) on 2008-Sep2

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene>

_E_x_a_m_p_l_e_s:

         # Convert the object to a list
         xx <- as.list(org.EcK12.egALIAS2EG)
         # Remove pathway identifiers that do not map to any entrez gene id
         xx <- xx[!is.na(xx)]
         if(length(xx) > 0){
             # The entrez gene identifiers for the first two elements of XX
             xx[1:2]
             # Get the first one
             xx[[1]]
         }

