agGO2ALLPROBES              package:ag              R Documentation

_M_a_p _B_e_t_w_e_e_n _G_e_n_e _O_n_t_o_l_o_g_y (_G_O) _I_d_e_n_t_i_f_i_e_r_s _a_n_d _a_l_l _M_a_n_u_f_a_c_t_u_r_e_r _I_d_e_n_t_i_f_i_e_r_s

_D_e_s_c_r_i_p_t_i_o_n:

     agGO2ALLPROBES is an R environment that provides mappings between
     a given GO id and all manufacturer ids.

_D_e_t_a_i_l_s:

     Each GO term maps to a named vector of manufacturer ids. The name
     associated with each manufacturer id corresponds to the evidence
     code for that GO id. The evidence code indicates what kind of
     evidence supports the association between the GO and Entrez Gene
     ids. Evidence codes currently in use include:

     IMP - inferred from mutant phenotype  

     IGI - inferred from genetic interaction

     IPI - inferred from physical interaction  

     ISS - inferred from sequence similarity  

     IDA - inferred from direct assay  

     IEP - inferred from expression pattern  

     IEA - inferred from electronic annotation  

     TAS - traceable author statement  

     NAS - non-traceable author statement  

     ND - no biological data available  

     IC - inferred by curator

     A GO id may be mapped to the same manufacturer id more than once
     but the evidence code can be different. Mappings between Gene
     Ontology ids and Gene Ontology terms and other information are
     available in a separate data package named GO.  

     Mappings were based on data provided:

     Entrez Gene:<URL:
     http://gopher5/compbio/annotationSourceData/ftp.ncbi.nlm.nih.gov/g
     ene/DATA/>. Built: Source data downloaded from Entrez Gene on Tue
     May 17 18:26:20 2005

     Package built Tue May 17 18:29:49 2005

_R_e_f_e_r_e_n_c_e_s:

     <URL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/>

_E_x_a_m_p_l_e_s:

         # Convert to a list
         xx <- as.list(agGO2ALLPROBES)
         if(length(xx) > 0){
             # Gets the probe ids for the top 2nd and 3nd GO ids
             goids <- xx[2:3]
             # Gets all the probe ids for the first element of goids
             goids[[1]]
             # Evidence code for the mappings
             names(goids[[1]])
         }

