hgu2beta7GO2ALLPROBES       package:hgu2beta7       R Documentation

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

     The Gene Ontology (GO) Consortium maintains a controlled
     vocabulary of defined terms to describe gene products. Each of the
     terms is assigned a GO id that can be associated with a group of
     genes directly or indirectly through the children GO ids of the GO
     id. hgu2beta7GO2ALLPROBES maps GO ids to genes (represented by
     probe identifiers) that are directly or indirectly mapped to the
     GO ids by traversing the GO tree.

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

     GO terminologies are presented as a directed acyclic graph with
     root nodes having more general terms than their children nodes.
     Therefore, a GO id can be mapped to genes corresponding to the
     term of that particular GO id as well as genes corresponding to
     the terms of all the children GO ids.

     hgu2beta7GO2ALLPROBES maps a GO id to all the probe ids
     representing genes mapped by traversing the GO tree. The mapped
     probe ids are named vectors. Names of the vectors are the evidence
     codes indicating what kind of evidence is found to support the
     association between GO ids and genes.

     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

     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
     and Gene Ontology terms and other information are available in a
     separate data package named GO.  

     Mappings were based on data provided:

     LocusLink:<URL:
     ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz>. Built:
     February 16, 2005

     Package built Wed Feb 16 23:32:20 2005

_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(hgu2beta7GO2ALLPROBES)
         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]])
         }

