agGO2PROBE                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) _a_n_d _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:

     agGO2PROBE is an R environment that provides mappings between GO
     identifiers and manufacturer identifiers.

_D_e_t_a_i_l_s:

     Each GO term maps to a named vector of manufacturer identifiers.
     The name associated with each manufacturer identifier corresponds
     to the evidence code for that GO identifier. The evidence code
     indicates what kind of evidence supports the association between
     the GO and Entrez Gene identifiers. 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 identifier may be mapped to the same probe identifier more
     than once but the evidence code can be different. Mappings between
     Gene Ontology identifiers an Gene Ontology terms and other
     information are available in a separate data package named GO. 

     Mappings were based on data provided by:

     Entrez Gene Tair: <URL:
     ftp://ftp.arabidopsis.org/home/tair/Microarrays/Affymetrix/affy_AG
     _array_elements-2006-07-14.txt> Tair: <URL:
     ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR_sequenced_genes>
     Tair: <URL:
     ftp://ftp.arabidopsis.org/home/tair/User_Requests/LocusPublished.0
     8012006.txt> Built: N/A.

     Package built Wed Sep  6 11:22:37 2006

_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(agGO2PROBE)
         if(length(xx) > 0){
             # Gets the probe identifiers for the top 2nd and 3nd GO identifiers
             goids <- xx[2:3]
             # Gets the probe identifiers for the first element of goids
             goids[[1]]
             # Evidence code for the mappings
             names(goids[[1]])
         }

