hgu2beta7ACCNUM          package:hgu2beta7          R Documentation

_M_a_p_p_i_n_g_s _b_e_t_w_e_e_n _p_r_o_b_e _i_d_e_n_t_i_f_i_e_r_s _a_n_d _m_a_n_u_f_a_c_t_u_r_e_r _o_r _u_s_e_r _p_r_o_v_i_d_e_d
_i_d_e_n_t_i_f_i_e_r_s

_D_e_s_c_r_i_p_t_i_o_n:

     hgu2beta7ACCNUM contains mappings between probe ids to identifiers
     provided by a manufacturer or user at the time when hgu2beta7 was
     built. The manufacture or user provided ids were used to link
     probe ids to annotation data available from various public data
     sources to obtain the other annotations contained in hgu2beta7.

_D_e_t_a_i_l_s:

     In order to build an annotate data package, a data file with a
     column for probe ids and another for the matching
     manufacturer/user provided ids is required. This data file is used
     as the base for mapping probe ids to LocusLink identifiers (unique
     ids used by NCBI <URL: http://www.ncbi.nlm.nih.gov/LocusLink/> to
     represent genetic loci and link to curated sequence and
     descriptive information) through the manufacturer/user provided
     ids. The mapped LocusLink ids then serve as the point of linkage
     to other annotation data provided by various public data sources.

     hgu2beta7ACCNUM contains the mappings of the base file and the
     derived mappings between probe ids to other annotation data are
     contained by other annotation data files in hgu2beta7. 

     Valid manufacturer/user provided ids currently include GenBank
     accession numbers (identifiers obtained after submitting a
     sequence to GenBank, EMBL or DDBJ), UniGene ids (identifiers used
     by NCBI to represent clusters of sequences of a unique gene),
     RefSeq ids (identifiers for non-redundant sequences curated by
     NCBI), or IMAGE clone ids (identifies given to clones from shared
     arrayed cDNA libraries by The Integrated Molecular Analysis of
     Gene Expression (IMAGE) Consortium).

     For all the Affymetrix chips, the manufacturer/user provided ids
     are GenBank accession numbers. 

     Package built: Wed Feb 16 23:32:20 2005

_E_x_a_m_p_l_e_s:

             # Convert to a list
             xx <- as.list(hgu2beta7ACCNUM)
             # Remove probe ids that do not map to any ACCNUM
             xx <- xx[!is.na(xx)]
             if(length(xx) > 0){
             # Get the ACCNUM for the first five probes
             xx[1:5]
             # Get the first one
             xx[[1]]
     }

