agREFSEQ                 package:ag                 R Documentation

_M_a_p _b_e_t_w_e_e_n _M_a_n_u_f_a_c_t_u_r_e_r _I_d_e_n_t_i_f_i_e_r_s _a_n_d _R_e_f_S_e_q _I_d_e_n_t_i_f_i_e_r_s

_D_e_s_c_r_i_p_t_i_o_n:

     agREFSEQ is an R environment that provides mappings between
     manufacturer ids and RefSeq ids.

_D_e_t_a_i_l_s:

     Each manufacturer id is mapped to a named vector of RefSeq ids.
     The name represents the manufacturer id and the vector contains
     all RefSeq ids that can be mapped to that manufacturer id. The
     length of the vector may be one or greater, depending on how many
     RefSeq ids a given manufacturer id can be mapped to. An 'NA' is
     reported for any manufacturer id that cannot be mapped to a RefSeq
     id at this time.

     RefSeq ids differ in format according to the type of record the
     ids are for as shown below:

     NG_XXXXX: RefSeq accessions for genomic region (nucleotide)
     records

     NM_XXXXX: RefSeq accessions for mRNA records

     NC_XXXXX: RefSeq accessions for chromosome records

     NP_XXXXX: RefSeq accessions for protein records

     XR_XXXXX: RefSeq accessions for model RNAs that are not associated
     with protein products

     XM_XXXXX: RefSeq accessions for model mRNA records

     XP_XXXXX: RefSeq accessions for model protein records

     Where XXXXX is a sequence of integers.

     NCBI <URL: http://www.ncbi.nlm.nih.gov/RefSeq/> allows users to
     query the RefSeq database using RefSeq ids.

     Mappings were based on data provided by:

     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: http://www.ncbi.nlm.nih.gov> <URL:
     http://www.ncbi.nlm.nih.gov/RefSeq/>

_E_x_a_m_p_l_e_s:

         # Convert the environment to a list
         xx <- as.list(agREFSEQ)
         # Remove probe ids that do not map to any RefSeq
         xx <- xx[!is.na(xx)]
         if(length(xx) > 0){
         # The RefSeq for the first two elements of XX
         xx[1:2]
         # Get the first one
         xx[[1]]
     }

