annaffyPATH             package:annaffy             R Documentation

_S_u_b_s_e_t _o_f _a_n_n_o_t_a_t_i_o_n _d_a_t_a _f_i_l_e _f_o_r _P_A_T_H _i_n _t_h_e _h_g_u_9_5_a_v_2 _p_a_c_k_a_g_e

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

     This is an R environment (hash table like) object containing key
     and value pairs for the mappings between probe identifiers (key)
     and pathway identifiers defined by KEGG (value). Keys can be
     accessed using ls(name of the environment) and values using
     get(key, name of the environment) or mget(keys, name of the
     environment). Values may be vectors of length 1 or greater
     depending on whether a given probe identifier can be associated
     with only one or more pathways. Mappings between probe ids and
     pathway ids were obtained their mappings to LocusLink ids. NA is
     assigned to probe identifiers that can not be  associated with any
     pathway at this time. Mappings between pathway ids to pathway
     names can be found in a separate data package named KEGG.

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

     Mappings were based on data provided by KEGG

     Source data built: KEGG built: Release 29.0 (January 2004).<URL:
     ftp://ftp.genome.ad.jp/pub/kegg/pathways>. Package built: Wed Jan
     14 22:11:08 2004 Contains 250 randomly selected probes

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

     <URL: ftp://ftp.genome.ad.jp/pub/kegg/pathways>

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

             require("annotate") || stop("annotate unavailable")
             xx <- ls(env = annaffyPATH)
             if(length(xx) > 0){
                     # Using get for value of the first key
                     get(xx[1], annaffyPATH )
                     #Using mget for a few keys
                     if(length(xx) >= 3){
                             mget(xx[1:3], annaffyPATH, ifnotfound=NA )
                             #Using lookUp of annotate(> 1.3.4)
                             lookUp(xx[1:3],"annaffy","PATH")
                     }
             }

