indacREFSEQ              package:indac              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:

     indacREFSEQ is an R environment that provides mappings between
     manufacturer identifiers and RefSeq identifiers.

_D_e_t_a_i_l_s:

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

     RefSeq identifiers differ in format according to the type of
     record the identifiers 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 identifiers.

     Mappings were based on data provided by:

     Entrez Gene:\<URL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/>. Built:
     Source data downloaded from Entrez Gene on Fri Aug 24 00:35:59
     2007

     Package built Fri Aug 24 00:42:00 2007

_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(indacREFSEQ)
         # Remove probe identifiers 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]]
     }

