hgu95av2GO2PROBE          package:hgu95av2          R Documentation

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_i_d_s

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

     A GO id can be associated with a group of genes directly.
     hgu95av2GO2PROBE maps each GO id to the genes represented by probe
     ids that are directly associated with the GO id.

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

     hgu95av2GO2PROBE is an environment object with key and value
     pairs. Keys are GO ids and values are the probe ids that are
     directly or associated with the GO ids. Values are vectors of
     length 1  or greater depending on whether a given GO id can be
     mapped to only one or more probe ids. Names for values are the
     evidence codes for the GO ids indicating what kind of evidence is
     found to support the association. The evidence codes 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

     GO ids can not be mapped to any probe identifier are assigned a
     value of NA. A GO id may be mapped to the same probe id more than
     once but the evidence code can be different. Mappings between Gene
     Ontology ids an Gene Ontology terms and other information are
     available in a separate data package named GO. 

     Mappings were based on data provided by:

     LocusLink LocusLink built: March  3, 2004. <URL:
     ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.ga>.

     Package built Wed Mar  3 16:27:29 2004

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

     <URL: ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz>

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

         # Convert to a list
         xx <- as.list(hgu95av2GO2PROBE)
         if(length(xx) > 0){
             # Gets the probe ids for the top 2nd and 3nd GO ids
             goids <- xx[2:3]
             # Gets the probe ids for the first element of goids
             goids[[1]]
             # Evidence code for the mappings
             names(goids[[1]])
         }

